@gmod/jbrowse/src/JBrowse/View/FileDialog/TrackList/_IndexedFileDriver.js

JBrowse - client-side genome browser

define([
           'dojo/_base/declare',
           'JBrowse/Util',
           'JBrowse/Model/FileBlob',
           'JBrowse/Model/XHRBlob'
       ],
       function( declare, Util, FileBlob, XHRBlob ) {
var uniqCounter = 0;
return declare( null, {

    tryResource: function( configs, resource ) {
        if( resource.type == this.fileExtension ) {
            var basename = Util.basename(
                resource.file ? resource.file.name :
                resource.url  ? resource.url       :
                                ''
            );
            if( !basename )
                return false;

            // go through the configs and see if there is one for an index that seems to match
            for( var n in configs ) {
                var c = configs[n];
                if( Util.basename( c[this.indexConfKey] ? c[this.indexConfKey ].url || c[this.indexConfKey].blob.name : c[this.indexUrlConfKey], '.'+this.indexExtension ) == basename ) {
                    // it's a match, put it in
                    c[this.fileConfKey] = this._makeBlob( resource );
                    return true;
                }
            }
            // go through again and look for index files that don't have the base extension in them
            basename = Util.basename( basename, '.'+this.fileExtension );
            for( var n in configs ) {
                var c = configs[n];
                if( Util.basename( c[this.indexConfKey] ? c[this.indexConfKey].url || c[this.indexConfKey].blob.name : c[this.indexUrlConfKey], '.'+this.indexExtension ) == basename ) {
                    // it's a match, put it in
                    c[this.fileConfKey] = this._makeBlob( resource );
                    return true;
                }
            }

            // otherwise make a new store config for it
            var newName = this.name+'_'+basename+'_'+uniqCounter++;
            configs[newName] = {
                type: this.storeType,
                name: newName,
                fileBasename: basename
            };
            configs[newName][this.fileConfKey] = this._makeBlob( resource );

            return true;
        } else if( resource.type == this.indexExtension ) {
            var basename = Util.basename(
                resource.file ? resource.file.name :
                resource.url  ? resource.url       :
                                ''
                , '.'+this.indexExtension
            );
            if( !basename )
                return false;

            // go through the configs and look for data files that match like zee.bam -> zee.bam.bai
            for( var n in configs ) {
                var c = configs[n];
                if( Util.basename( c[this.fileConfKey] ? c[this.fileConfKey].url || c[this.fileConfKey].blob.name : c[this.fileUrlConfKey] ) == basename ) {
                    // it's a match, put it in
                    c[this.indexConfKey] = this._makeBlob( resource );
                    return true;
                }
            }
            // go through again and look for data files that match like zee.bam -> zee.bai
            for( var n in configs ) {
                var c = configs[n];
                if( Util.basename( c[this.fileConfKey] ? c[this.fileConfKey].url || c[this.fileConfKey].blob.name : c[this.fileUrlConfKey], '.'+this.fileExtension ) == basename ) {
                    // it's a match, put it in
                    c[this.indexConfKey] = this._makeBlob( resource );
                    return true;
                }
            }

            // otherwise make a new store
            var newName = this.name+'_'+Util.basename(basename,'.'+this.fileExtension)+'_'+uniqCounter++;
            configs[newName] = {
                name: newName,
                type: this.storeType
            };

            configs[newName][this.indexConfKey] = this._makeBlob( resource );
            return true;
        }
        else
            return false;
    },

    // try to merge any singleton file and index stores.  currently can only do this if there is one of each
    finalizeConfiguration: function( configs ) {
        var singletonIndexes = {};
        var singletonIndexCount = 0;
        var singletonFiles = {};
        var singletonFileCount = 0;
        for( var n in configs ) {
            var conf = configs[n];
            if( conf.type === this.storeType ) {
                if( (conf[this.indexConfKey] || conf[this.indexUrlConfKey]) && ! ( conf[this.fileConfKey] || conf[this.fileUrlConfKey] ) ) {
                    // singleton Index
                    singletonIndexCount++;
                    singletonIndexes[n] = conf;
                }
                else if(( conf[this.fileConfKey] || conf[this.fileUrlConfKey] ) && ! ( conf[this.indexConfKey] || conf[this.indexUrlConfKey]) ) {
                    // singleton File
                    singletonFileCount++;
                    singletonFiles[n] = conf;
                }
            }
        }

        // if we have a single File and single Index left at the end,
        // stick them together and we'll see what happens
        if( singletonFileCount == 1 && singletonIndexCount == 1 ) {
            for( var indexName in singletonIndexes ) {
                for( var fileName in singletonFiles ) {
                    if( singletonIndexes[indexName][this.indexUrlConfKey] )
                        singletonFiles[fileName][this.indexUrlConfKey] = singletonIndexes[indexName][this.indexUrlConfKey];
                    if( singletonIndexes[indexName][this.indexConfKey] )
                        singletonFiles[fileName][this.indexConfKey] = singletonIndexes[indexName][this.indexConfKey];

                    delete configs[indexName];
                }
            }
        }

        // delete any remaining singleton Indexes, since they don't have
        // a hope of working
        for( var indexName in singletonIndexes ) {
            delete configs[indexName];
        }

        // delete any remaining singleton Files, unless they are URLs
        for( var fileName in singletonFiles ) {
            if( ! configs[fileName][this.fileUrlConfKey] )
                delete configs[fileName];
        }
    },

    _makeBlob: function( resource ) {
        var r = resource.file ? new FileBlob( resource.file ) :
                resource.url  ? new XHRBlob( resource.url )   :
                                null;
        if( ! r )
            throw 'unknown resource type';
        return r;

    },

    confIsValid: function( conf ) {
        return (conf[this.fileConfKey] || conf[this.fileUrlConfKey]) && ( conf[this.indexConfKey] || conf[this.indexUrlConfKey] || conf[this.fileUrlConfKey] );
    }
});
});