commit/galaxy-central: carlfeberhard: UI, paired collection creator: refactor autopairing and add tests
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/581d871b8102/ Changeset: 581d871b8102 User: carlfeberhard Date: 2015-02-10 23:15:43+00:00 Summary: UI, paired collection creator: refactor autopairing and add tests Affected #: 4 files diff -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e -r 581d871b810205f6a02e994983ffe316e206b746 client/galaxy/scripts/mvc/collection/paired-collection-creator.js --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -3,7 +3,7 @@ "utils/natural-sort", "mvc/base-mvc", "utils/localization" -], function( levelshteinDistance, naturalSort, baseMVC, _l ){ +], function( levenshteinDistance, naturalSort, baseMVC, _l ){ /* ============================================================================ TODO: _adjPairedOnScrollBar @@ -28,7 +28,6 @@ className : 'dataset paired', initialize : function( attributes ){ - //console.debug( 'PairView.initialize:', attributes ); this.pair = attributes.pair || {}; }, @@ -46,9 +45,6 @@ .data( 'pair', this.pair ) .html( this.template({ pair: this.pair }) ) .addClass( 'flex-column-container' ); - -//TODO: would be good to get the unpair-btn into this view - but haven't found a way with css - return this; }, @@ -61,24 +57,17 @@ /** dragging pairs for re-ordering */ _dragstart : function( ev ){ - //console.debug( this, '_dragstartPair', ev ); ev.currentTarget.style.opacity = '0.4'; if( ev.originalEvent ){ ev = ev.originalEvent; } ev.dataTransfer.effectAllowed = 'move'; ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.pair ) ); - //ev.dataTransfer.setDragImage( null, 0, 0 ); - - // the canvas can be used to create the image - //ev.dataTransfer.setDragImage( canvasCrossHairs(), 25, 25 ); - - //console.debug( 'ev.dataTransfer:', ev.dataTransfer ); this.$el.parent().trigger( 'pair.dragstart', [ this ] ); }, + /** dragging pairs for re-ordering */ _dragend : function( ev ){ - //console.debug( this, '_dragendPair', ev ); ev.currentTarget.style.opacity = '1.0'; this.$el.parent().trigger( 'pair.dragend', [ this ] ); }, @@ -92,8 +81,106 @@ toString : function(){ return 'PairView(' + this.pair.name + ')'; } +}); -}); + +/** returns an autopair function that uses the provided options.match function */ +function autoPairFnBuilder( options ){ + options = options || {}; + options.createPair = options.createPair || function _defaultCreatePair( params ){ + this.debug( 'creating pair:', params.listA[ params.indexA ].name, params.listB[ params.indexB ].name ); + params = params || {}; + return this._pair( + params.listA.splice( params.indexA, 1 )[0], + params.listB.splice( params.indexB, 1 )[0], + { silent: true } + ); + }; + // compile these here outside of the loop + var _regexps = []; + function getRegExps(){ + if( !_regexps.length ){ + _regexps = [ + new RegExp( this.filters[0] ), + new RegExp( this.filters[1] ) + ]; + } + return _regexps; + } + // mangle params as needed + options.preprocessMatch = options.preprocessMatch || function _defaultPreprocessMatch( params ){ + var regexps = getRegExps.call( this ); + return _.extend( params, { + matchTo : params.matchTo.name.replace( regexps[0], '' ), + possible : params.possible.name.replace( regexps[1], '' ) + }); + }; + + return function _strategy( params ){ + this.debug( 'autopair _strategy ---------------------------' ); + params = params || {}; + var listA = params.listA, + listB = params.listB, + indexA = 0, indexB, + bestMatch = { + score : 0.0, + index : null + }, + paired = []; + //console.debug( 'params:', JSON.stringify( params, null, ' ' ) ); + this.debug( 'starting list lens:', listA.length, listB.length ); + this.debug( 'bestMatch (starting):', JSON.stringify( bestMatch, null, ' ' ) ); + + while( indexA < listA.length ){ + var matchTo = listA[ indexA ]; + bestMatch.score = 0.0; + + for( indexB=0; indexB<listB.length; indexB++ ){ + var possible = listB[ indexB ]; + this.debug( indexA + ':' + matchTo.name ); + this.debug( indexB + ':' + possible.name ); + + // no matching with self + if( listA[ indexA ] !== listB[ indexB ] ){ + bestMatch = options.match.call( this, options.preprocessMatch.call( this, { + matchTo : matchTo, + possible: possible, + index : indexB, + bestMatch : bestMatch + })); + this.debug( 'bestMatch:', JSON.stringify( bestMatch, null, ' ' ) ); + if( bestMatch.score === 1.0 ){ + this.debug( 'breaking early due to perfect match' ); + break; + } + } + } + var scoreThreshold = options.scoreThreshold.call( this ); + this.debug( 'scoreThreshold:', scoreThreshold ); + this.debug( 'bestMatch.score:', bestMatch.score ); + + if( bestMatch.score >= scoreThreshold ){ + this.debug( 'creating pair' ); + paired.push( options.createPair.call( this, { + listA : listA, + indexA : indexA, + listB : listB, + indexB : bestMatch.index + })); + this.debug( 'list lens now:', listA.length, listB.length ); + } else { + indexA += 1; + } + if( !listA.length || !listB.length ){ + return paired; + } + } + this.debug( 'paired:', JSON.stringify( paired, null, ' ' ) ); + this.debug( 'autopair _strategy ---------------------------' ); + return paired; + }; +} + /** An interface for building collections of paired datasets. */ @@ -108,15 +195,11 @@ attributes = _.defaults( attributes, { datasets : [], filters : this.DEFAULT_FILTERS, - //automaticallyPair : false, automaticallyPair : true, - matchPercentage : 1.0, - //matchPercentage : 0.9, - //matchPercentage : 0.8, - //strategy : 'levenshtein' - strategy : 'lcs' + strategy : 'lcs', + matchPercentage : 0.9, + twoPassAutopairing : true }); - //this.debug( 'attributes now:', attributes ); /** unordered, original list */ this.initialList = attributes.datasets; @@ -133,15 +216,18 @@ /** try to auto pair the unpaired datasets on load? */ this.automaticallyPair = attributes.automaticallyPair; - /** distance/mismatch level allowed for autopairing */ - this.matchPercentage = attributes.matchPercentage; - /** what method to use for auto pairing (will be passed aggression level) */ this.strategy = this.strategies[ attributes.strategy ] || this.strategies[ this.DEFAULT_STRATEGY ]; if( _.isFunction( attributes.strategy ) ){ this.strategy = attributes.strategy; } + /** distance/mismatch level allowed for autopairing */ + this.matchPercentage = attributes.matchPercentage; + + /** try to autopair using simple first, then this.strategy on the remainder */ + this.twoPassAutopairing = attributes.twoPassAutopairing; + /** remove file extensions (\.*) from created pair names? */ this.removeExtensions = true; //this.removeExtensions = false; @@ -173,12 +259,12 @@ }, /** which commonFilter to use by default */ DEFAULT_FILTERS : 'illumina', - //DEFAULT_FILTERS : 'none', /** map of name->fn for autopairing */ strategies : { - 'lcs' : 'autoPairLCSs', - 'levenshtein' : 'autoPairLevenshtein' + 'simple' : 'autopairSimple', + 'lcs' : 'autopairLCS', + 'levenshtein' : 'autopairLevenshtein' }, /** default autopair strategy name */ DEFAULT_STRATEGY : 'lcs', @@ -191,8 +277,6 @@ this.paired = []; this.unpaired = []; - //this.fwdSelectedIds = []; - //this.revSelectedIds = []; this.selectedIds = []; // sort initial list, add ids if needed, and save new working copy to unpaired @@ -212,7 +296,6 @@ _sortInitialList : function(){ //this.debug( '-- _sortInitialList' ); this._sortDatasetList( this.initialList ); - //this._printList( this.unpaired ); }, /** sort a list of datasets */ @@ -229,39 +312,31 @@ dataset.id = _.uniqueId(); } }); - //this._printList( this.unpaired ); return this.initialList; }, /** split initial list into two lists, those that pass forward filters & those passing reverse */ - _splitByFilters : function( filters ){ - var fwd = [], - rev = []; + _splitByFilters : function(){ + var regexFilters = this.filters.map( function( stringFilter ){ + return new RegExp( stringFilter ); + }), + split = [ [], [] ]; - function _addToFwdOrRev( unpaired ){ - if( this._filterFwdFn( unpaired ) ){ - fwd.push( unpaired ); - } - if( this._filterRevFn( unpaired ) ){ - rev.push( unpaired ); - } + function _filter( unpaired, filter ){ + return filter.test( unpaired.name ); + //return dataset.name.indexOf( filter ) >= 0; } - this.unpaired.forEach( _.bind( _addToFwdOrRev, this ) ); - return [ fwd, rev ]; - }, - - /** filter fn to apply to forward datasets */ - _filterFwdFn : function( dataset ){ -//TODO: this treats *all* strings as regex which may confuse people - var regexp = new RegExp( this.filters[0] ); - return regexp.test( dataset.name ); - //return dataset.name.indexOf( this.filters[0] ) >= 0; - }, - - /** filter fn to apply to reverse datasets */ - _filterRevFn : function( dataset ){ - var regexp = new RegExp( this.filters[1] ); - return regexp.test( dataset.name ); + this.unpaired.forEach( function _filterEach( unpaired ){ + // 90% of the time this seems to work, but: + //TODO: this treats *all* strings as regex which may confuse people - possibly check for // surrounding? + // would need explanation in help as well + regexFilters.forEach( function( filter, i ){ + if( _filter( unpaired, filter ) ){ + split[i].push( unpaired ); + } + }); + }); + return split; }, /** add a dataset to the unpaired list in it's proper order */ @@ -288,202 +363,79 @@ }, // ------------------------------------------------------------------------ auto pairing -//TODO: lots of boiler plate btwn the three auto pair fns /** two passes to automatically create pairs: * use both simpleAutoPair, then the fn mentioned in strategy */ autoPair : function( strategy ){ + // split first using exact matching + var split = this._splitByFilters(), + paired = []; + if( this.twoPassAutopairing ){ + paired = this.autopairSimple({ + listA : split[0], + listB : split[1] + }); + split = this._splitByFilters(); + } + + // uncomment to see printlns while running tests + //this.debug = function(){ console.log.apply( console, arguments ); }; + + // then try the remainder with something less strict strategy = strategy || this.strategy; - //this.debug( '-- autoPair', strategy ); - var paired = this.simpleAutoPair(); - paired = paired.concat( this[ strategy ].call( this ) ); + split = this._splitByFilters(); + paired = paired.concat( this[ strategy ].call( this, { + listA : split[0], + listB : split[1] + })); return paired; }, - /** attempts to pair forward with reverse when names exactly match (after removing filters) */ - simpleAutoPair : function(){ - //this.debug( '-- simpleAutoPair' ); - // simplified auto pair that moves down unpaired lists *in order*, - // removes filters' strings from fwd and rev, - // and, if names w/o filters *exactly* match, creates a pair - // possibly good as a first pass - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - matchFound = false, - paired = []; + autopairSimple : autoPairFnBuilder({ + scoreThreshold: function(){ return 1.0; }, + match : function _match( params ){ + params = params || {}; + if( params.matchTo === params.possible ){ + return { + index: params.index, + score: 1.0 + }; + } + return params.bestMatch; + } + }), - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - //TODO: go through the filterFwdFn - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - matchFound = false; + autopairLevenshtein : autoPairFnBuilder({ + scoreThreshold: function(){ return this.matchPercentage; }, + match : function _matches( params ){ + params = params || {}; + var distance = levenshteinDistance( params.matchTo, params.possible ), + score = 1.0 - ( distance / ( Math.max( params.matchTo.length, params.possible.length ) ) ); + if( score > params.bestMatch.score ){ + return { + index: params.index, + score: score + }; + } + return params.bestMatch; + } + }), - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev && fwdName === revName ){ - matchFound = true; - // if it is a match, keep i at current, pop fwd, pop rev and break - //this.debug( '---->', fwdName, revName ); - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( j, 1 )[0], - { silent: true } - ); - paired.push( pair ); - break; - } + autopairLCS : autoPairFnBuilder({ + scoreThreshold: function(){ return this.matchPercentage; }, + match : function _matches( params ){ + params = params || {}; + var match = this._naiveStartingAndEndingLCS( params.matchTo, params.possible ).length, + score = match / ( Math.max( params.matchTo.length, params.possible.length ) ); + if( score > params.bestMatch.score ){ + return { + index: params.index, + score: score + }; } - if( !matchFound ){ i += 1; } + return params.bestMatch; } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, - - /** attempt to autopair using edit distance between forward and reverse (after removing filters) */ - autoPairLevenshtein : function(){ - //precondition: filters are set, both lists are not empty, and all filenames.length > filters[?].length - //this.debug( '-- autoPairLevenshtein' ); - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - distance, bestIndex, bestDist, - paired = []; - - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - //TODO: go through the filterFwdFn - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - bestDist = Number.MAX_VALUE; - - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev ){ - if( fwdName === revName ){ - //this.debug( '\t\t exactmatch:', fwdName, revName ); - bestIndex = j; - bestDist = 0; - break; - } - distance = levenshteinDistance( fwdName, revName ); - //this.debug( '\t\t distance:', distance, 'bestDist:', bestDist ); - if( distance < bestDist ){ - bestIndex = j; - bestDist = distance; - } - } - } - //this.debug( '---->', fwd.name, bestIndex, bestDist ); - //this.debug( '---->', fwd.name, revList[ bestIndex ].name, bestDist ); - - var percentage = 1.0 - ( bestDist / ( Math.max( fwdName.length, revName.length ) ) ); - //this.debug( '----> %', percentage * 100 ); - - if( percentage >= this.matchPercentage ){ - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( bestIndex, 1 )[0], - { silent: true } - ); - paired.push( pair ); - if( fwdList.length <= 0 || revList.length <= 0 ){ - return paired; - } - } else { - i += 1; - } - } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, - - /** attempt to auto pair using common substrings from both front and back (after removing filters) */ - autoPairLCSs : function(){ - //precondition: filters are set, both lists are not empty - //this.debug( '-- autoPairLCSs' ); - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - currMatch, bestIndex, bestMatch, - paired = []; - if( !fwdList.length || !revList.length ){ return paired; } - //this.debug( fwdList, revList ); - - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - bestMatch = 0; - - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev ){ - if( fwdName === revName ){ - //this.debug( '\t\t exactmatch:', fwdName, revName ); - bestIndex = j; - bestMatch = fwdName.length; - break; - } - var match = this._naiveStartingAndEndingLCS( fwdName, revName ); - currMatch = match.length; - //this.debug( '\t\t match:', match, 'currMatch:', currMatch, 'bestMatch:', bestMatch ); - if( currMatch > bestMatch ){ - bestIndex = j; - bestMatch = currMatch; - } - } - } - //this.debug( '---->', i, fwd.name, bestIndex, revList[ bestIndex ].name, bestMatch ); - - var percentage = bestMatch / ( Math.min( fwdName.length, revName.length ) ); - //this.debug( '----> %', percentage * 100 ); - - if( percentage >= this.matchPercentage ){ - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( bestIndex, 1 )[0], - { silent: true } - ); - paired.push( pair ); - if( fwdList.length <= 0 || revList.length <= 0 ){ - return paired; - } - } else { - i += 1; - } - } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, + }), /** return the concat'd longest common prefix and suffix from two strings */ _naiveStartingAndEndingLCS : function( s1, s2 ){ @@ -1338,19 +1290,19 @@ // ........................................................................ paired - drag and drop re-ordering //_dragenterPairedColumns : function( ev ){ - // console.debug( '_dragenterPairedColumns:', ev ); + // this.debug( '_dragenterPairedColumns:', ev ); //}, //_dragleavePairedColumns : function( ev ){ - // //console.debug( '_dragleavePairedColumns:', ev ); + // //this.debug( '_dragleavePairedColumns:', ev ); //}, /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */ _dragoverPairedColumns : function( ev ){ - //console.debug( '_dragoverPairedColumns:', ev ); + //this.debug( '_dragoverPairedColumns:', ev ); ev.preventDefault(); var $list = this.$( '.paired-columns .column-datasets' ); this._checkForAutoscroll( $list, ev.originalEvent.clientY ); - //console.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); + //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY ); $( '.paired-drop-placeholder' ).remove(); @@ -1369,7 +1321,7 @@ scrollTop = $element.scrollTop(), upperDist = y - offset.top, lowerDist = ( offset.top + $element.outerHeight() ) - y; - //console.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); + //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); if( upperDist >= 0 && upperDist < this.autoscrollDist ){ $element.scrollTop( scrollTop - AUTOSCROLL_SPEED ); } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){ @@ -1388,7 +1340,7 @@ top = $li.offset().top, halfHeight = Math.floor( $li.outerHeight() / 2 ) + WIGGLE; if( top + halfHeight > y && top - halfHeight < y ){ - //console.debug( y, top + halfHeight, top - halfHeight ) + //this.debug( y, top + halfHeight, top - halfHeight ) return $li; } } @@ -1419,13 +1371,13 @@ this.$( '.paired-columns .dataset.paired' ).each( function(){ newPaired.push( $( this ).data( 'pair' ) ); }); - //console.debug( newPaired ); + //this.debug( newPaired ); this.paired = newPaired; this._renderPaired(); }, /** drag communication with pair sub-views: dragstart */ _pairDragstart : function( ev, pair ){ - //console.debug( '_pairDragstart', ev, pair ) + //this.debug( '_pairDragstart', ev, pair ) // auto select the pair causing the event and move all selected pair.$el.addClass( 'selected' ); var $selected = this.$( '.paired-columns .dataset.selected' ); @@ -1433,7 +1385,7 @@ }, /** drag communication with pair sub-views: dragend - remove the placeholder */ _pairDragend : function( ev, pair ){ - //console.debug( '_pairDragend', ev, pair ) + //this.debug( '_pairDragend', ev, pair ) $( '.paired-drop-placeholder' ).remove(); this.$dragging = null; }, @@ -1736,7 +1688,6 @@ //============================================================================= /** a modal version of the paired collection creator */ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){ - console.log( datasets ); options = _.defaults( options || {}, { datasets : datasets, diff -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e -r 581d871b810205f6a02e994983ffe316e206b746 static/scripts/mvc/collection/paired-collection-creator.js --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -3,7 +3,7 @@ "utils/natural-sort", "mvc/base-mvc", "utils/localization" -], function( levelshteinDistance, naturalSort, baseMVC, _l ){ +], function( levenshteinDistance, naturalSort, baseMVC, _l ){ /* ============================================================================ TODO: _adjPairedOnScrollBar @@ -28,7 +28,6 @@ className : 'dataset paired', initialize : function( attributes ){ - //console.debug( 'PairView.initialize:', attributes ); this.pair = attributes.pair || {}; }, @@ -46,9 +45,6 @@ .data( 'pair', this.pair ) .html( this.template({ pair: this.pair }) ) .addClass( 'flex-column-container' ); - -//TODO: would be good to get the unpair-btn into this view - but haven't found a way with css - return this; }, @@ -61,24 +57,17 @@ /** dragging pairs for re-ordering */ _dragstart : function( ev ){ - //console.debug( this, '_dragstartPair', ev ); ev.currentTarget.style.opacity = '0.4'; if( ev.originalEvent ){ ev = ev.originalEvent; } ev.dataTransfer.effectAllowed = 'move'; ev.dataTransfer.setData( 'text/plain', JSON.stringify( this.pair ) ); - //ev.dataTransfer.setDragImage( null, 0, 0 ); - - // the canvas can be used to create the image - //ev.dataTransfer.setDragImage( canvasCrossHairs(), 25, 25 ); - - //console.debug( 'ev.dataTransfer:', ev.dataTransfer ); this.$el.parent().trigger( 'pair.dragstart', [ this ] ); }, + /** dragging pairs for re-ordering */ _dragend : function( ev ){ - //console.debug( this, '_dragendPair', ev ); ev.currentTarget.style.opacity = '1.0'; this.$el.parent().trigger( 'pair.dragend', [ this ] ); }, @@ -92,8 +81,106 @@ toString : function(){ return 'PairView(' + this.pair.name + ')'; } +}); -}); + +/** returns an autopair function that uses the provided options.match function */ +function autoPairFnBuilder( options ){ + options = options || {}; + options.createPair = options.createPair || function _defaultCreatePair( params ){ + this.debug( 'creating pair:', params.listA[ params.indexA ].name, params.listB[ params.indexB ].name ); + params = params || {}; + return this._pair( + params.listA.splice( params.indexA, 1 )[0], + params.listB.splice( params.indexB, 1 )[0], + { silent: true } + ); + }; + // compile these here outside of the loop + var _regexps = []; + function getRegExps(){ + if( !_regexps.length ){ + _regexps = [ + new RegExp( this.filters[0] ), + new RegExp( this.filters[1] ) + ]; + } + return _regexps; + } + // mangle params as needed + options.preprocessMatch = options.preprocessMatch || function _defaultPreprocessMatch( params ){ + var regexps = getRegExps.call( this ); + return _.extend( params, { + matchTo : params.matchTo.name.replace( regexps[0], '' ), + possible : params.possible.name.replace( regexps[1], '' ) + }); + }; + + return function _strategy( params ){ + this.debug( 'autopair _strategy ---------------------------' ); + params = params || {}; + var listA = params.listA, + listB = params.listB, + indexA = 0, indexB, + bestMatch = { + score : 0.0, + index : null + }, + paired = []; + //console.debug( 'params:', JSON.stringify( params, null, ' ' ) ); + this.debug( 'starting list lens:', listA.length, listB.length ); + this.debug( 'bestMatch (starting):', JSON.stringify( bestMatch, null, ' ' ) ); + + while( indexA < listA.length ){ + var matchTo = listA[ indexA ]; + bestMatch.score = 0.0; + + for( indexB=0; indexB<listB.length; indexB++ ){ + var possible = listB[ indexB ]; + this.debug( indexA + ':' + matchTo.name ); + this.debug( indexB + ':' + possible.name ); + + // no matching with self + if( listA[ indexA ] !== listB[ indexB ] ){ + bestMatch = options.match.call( this, options.preprocessMatch.call( this, { + matchTo : matchTo, + possible: possible, + index : indexB, + bestMatch : bestMatch + })); + this.debug( 'bestMatch:', JSON.stringify( bestMatch, null, ' ' ) ); + if( bestMatch.score === 1.0 ){ + this.debug( 'breaking early due to perfect match' ); + break; + } + } + } + var scoreThreshold = options.scoreThreshold.call( this ); + this.debug( 'scoreThreshold:', scoreThreshold ); + this.debug( 'bestMatch.score:', bestMatch.score ); + + if( bestMatch.score >= scoreThreshold ){ + this.debug( 'creating pair' ); + paired.push( options.createPair.call( this, { + listA : listA, + indexA : indexA, + listB : listB, + indexB : bestMatch.index + })); + this.debug( 'list lens now:', listA.length, listB.length ); + } else { + indexA += 1; + } + if( !listA.length || !listB.length ){ + return paired; + } + } + this.debug( 'paired:', JSON.stringify( paired, null, ' ' ) ); + this.debug( 'autopair _strategy ---------------------------' ); + return paired; + }; +} + /** An interface for building collections of paired datasets. */ @@ -108,15 +195,11 @@ attributes = _.defaults( attributes, { datasets : [], filters : this.DEFAULT_FILTERS, - //automaticallyPair : false, automaticallyPair : true, - matchPercentage : 1.0, - //matchPercentage : 0.9, - //matchPercentage : 0.8, - //strategy : 'levenshtein' - strategy : 'lcs' + strategy : 'lcs', + matchPercentage : 0.9, + twoPassAutopairing : true }); - //this.debug( 'attributes now:', attributes ); /** unordered, original list */ this.initialList = attributes.datasets; @@ -133,15 +216,18 @@ /** try to auto pair the unpaired datasets on load? */ this.automaticallyPair = attributes.automaticallyPair; - /** distance/mismatch level allowed for autopairing */ - this.matchPercentage = attributes.matchPercentage; - /** what method to use for auto pairing (will be passed aggression level) */ this.strategy = this.strategies[ attributes.strategy ] || this.strategies[ this.DEFAULT_STRATEGY ]; if( _.isFunction( attributes.strategy ) ){ this.strategy = attributes.strategy; } + /** distance/mismatch level allowed for autopairing */ + this.matchPercentage = attributes.matchPercentage; + + /** try to autopair using simple first, then this.strategy on the remainder */ + this.twoPassAutopairing = attributes.twoPassAutopairing; + /** remove file extensions (\.*) from created pair names? */ this.removeExtensions = true; //this.removeExtensions = false; @@ -173,12 +259,12 @@ }, /** which commonFilter to use by default */ DEFAULT_FILTERS : 'illumina', - //DEFAULT_FILTERS : 'none', /** map of name->fn for autopairing */ strategies : { - 'lcs' : 'autoPairLCSs', - 'levenshtein' : 'autoPairLevenshtein' + 'simple' : 'autopairSimple', + 'lcs' : 'autopairLCS', + 'levenshtein' : 'autopairLevenshtein' }, /** default autopair strategy name */ DEFAULT_STRATEGY : 'lcs', @@ -191,8 +277,6 @@ this.paired = []; this.unpaired = []; - //this.fwdSelectedIds = []; - //this.revSelectedIds = []; this.selectedIds = []; // sort initial list, add ids if needed, and save new working copy to unpaired @@ -212,7 +296,6 @@ _sortInitialList : function(){ //this.debug( '-- _sortInitialList' ); this._sortDatasetList( this.initialList ); - //this._printList( this.unpaired ); }, /** sort a list of datasets */ @@ -229,39 +312,31 @@ dataset.id = _.uniqueId(); } }); - //this._printList( this.unpaired ); return this.initialList; }, /** split initial list into two lists, those that pass forward filters & those passing reverse */ - _splitByFilters : function( filters ){ - var fwd = [], - rev = []; + _splitByFilters : function(){ + var regexFilters = this.filters.map( function( stringFilter ){ + return new RegExp( stringFilter ); + }), + split = [ [], [] ]; - function _addToFwdOrRev( unpaired ){ - if( this._filterFwdFn( unpaired ) ){ - fwd.push( unpaired ); - } - if( this._filterRevFn( unpaired ) ){ - rev.push( unpaired ); - } + function _filter( unpaired, filter ){ + return filter.test( unpaired.name ); + //return dataset.name.indexOf( filter ) >= 0; } - this.unpaired.forEach( _.bind( _addToFwdOrRev, this ) ); - return [ fwd, rev ]; - }, - - /** filter fn to apply to forward datasets */ - _filterFwdFn : function( dataset ){ -//TODO: this treats *all* strings as regex which may confuse people - var regexp = new RegExp( this.filters[0] ); - return regexp.test( dataset.name ); - //return dataset.name.indexOf( this.filters[0] ) >= 0; - }, - - /** filter fn to apply to reverse datasets */ - _filterRevFn : function( dataset ){ - var regexp = new RegExp( this.filters[1] ); - return regexp.test( dataset.name ); + this.unpaired.forEach( function _filterEach( unpaired ){ + // 90% of the time this seems to work, but: + //TODO: this treats *all* strings as regex which may confuse people - possibly check for // surrounding? + // would need explanation in help as well + regexFilters.forEach( function( filter, i ){ + if( _filter( unpaired, filter ) ){ + split[i].push( unpaired ); + } + }); + }); + return split; }, /** add a dataset to the unpaired list in it's proper order */ @@ -288,202 +363,79 @@ }, // ------------------------------------------------------------------------ auto pairing -//TODO: lots of boiler plate btwn the three auto pair fns /** two passes to automatically create pairs: * use both simpleAutoPair, then the fn mentioned in strategy */ autoPair : function( strategy ){ + // split first using exact matching + var split = this._splitByFilters(), + paired = []; + if( this.twoPassAutopairing ){ + paired = this.autopairSimple({ + listA : split[0], + listB : split[1] + }); + split = this._splitByFilters(); + } + + // uncomment to see printlns while running tests + //this.debug = function(){ console.log.apply( console, arguments ); }; + + // then try the remainder with something less strict strategy = strategy || this.strategy; - //this.debug( '-- autoPair', strategy ); - var paired = this.simpleAutoPair(); - paired = paired.concat( this[ strategy ].call( this ) ); + split = this._splitByFilters(); + paired = paired.concat( this[ strategy ].call( this, { + listA : split[0], + listB : split[1] + })); return paired; }, - /** attempts to pair forward with reverse when names exactly match (after removing filters) */ - simpleAutoPair : function(){ - //this.debug( '-- simpleAutoPair' ); - // simplified auto pair that moves down unpaired lists *in order*, - // removes filters' strings from fwd and rev, - // and, if names w/o filters *exactly* match, creates a pair - // possibly good as a first pass - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - matchFound = false, - paired = []; + autopairSimple : autoPairFnBuilder({ + scoreThreshold: function(){ return 1.0; }, + match : function _match( params ){ + params = params || {}; + if( params.matchTo === params.possible ){ + return { + index: params.index, + score: 1.0 + }; + } + return params.bestMatch; + } + }), - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - //TODO: go through the filterFwdFn - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - matchFound = false; + autopairLevenshtein : autoPairFnBuilder({ + scoreThreshold: function(){ return this.matchPercentage; }, + match : function _matches( params ){ + params = params || {}; + var distance = levenshteinDistance( params.matchTo, params.possible ), + score = 1.0 - ( distance / ( Math.max( params.matchTo.length, params.possible.length ) ) ); + if( score > params.bestMatch.score ){ + return { + index: params.index, + score: score + }; + } + return params.bestMatch; + } + }), - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev && fwdName === revName ){ - matchFound = true; - // if it is a match, keep i at current, pop fwd, pop rev and break - //this.debug( '---->', fwdName, revName ); - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( j, 1 )[0], - { silent: true } - ); - paired.push( pair ); - break; - } + autopairLCS : autoPairFnBuilder({ + scoreThreshold: function(){ return this.matchPercentage; }, + match : function _matches( params ){ + params = params || {}; + var match = this._naiveStartingAndEndingLCS( params.matchTo, params.possible ).length, + score = match / ( Math.max( params.matchTo.length, params.possible.length ) ); + if( score > params.bestMatch.score ){ + return { + index: params.index, + score: score + }; } - if( !matchFound ){ i += 1; } + return params.bestMatch; } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, - - /** attempt to autopair using edit distance between forward and reverse (after removing filters) */ - autoPairLevenshtein : function(){ - //precondition: filters are set, both lists are not empty, and all filenames.length > filters[?].length - //this.debug( '-- autoPairLevenshtein' ); - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - distance, bestIndex, bestDist, - paired = []; - - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - //TODO: go through the filterFwdFn - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - bestDist = Number.MAX_VALUE; - - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev ){ - if( fwdName === revName ){ - //this.debug( '\t\t exactmatch:', fwdName, revName ); - bestIndex = j; - bestDist = 0; - break; - } - distance = levenshteinDistance( fwdName, revName ); - //this.debug( '\t\t distance:', distance, 'bestDist:', bestDist ); - if( distance < bestDist ){ - bestIndex = j; - bestDist = distance; - } - } - } - //this.debug( '---->', fwd.name, bestIndex, bestDist ); - //this.debug( '---->', fwd.name, revList[ bestIndex ].name, bestDist ); - - var percentage = 1.0 - ( bestDist / ( Math.max( fwdName.length, revName.length ) ) ); - //this.debug( '----> %', percentage * 100 ); - - if( percentage >= this.matchPercentage ){ - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( bestIndex, 1 )[0], - { silent: true } - ); - paired.push( pair ); - if( fwdList.length <= 0 || revList.length <= 0 ){ - return paired; - } - } else { - i += 1; - } - } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, - - /** attempt to auto pair using common substrings from both front and back (after removing filters) */ - autoPairLCSs : function(){ - //precondition: filters are set, both lists are not empty - //this.debug( '-- autoPairLCSs' ); - var i = 0, j, - split = this._splitByFilters(), - fwdList = split[0], - revList = split[1], - fwdName, revName, - currMatch, bestIndex, bestMatch, - paired = []; - if( !fwdList.length || !revList.length ){ return paired; } - //this.debug( fwdList, revList ); - - while( i<fwdList.length ){ - var fwd = fwdList[ i ]; - fwdName = fwd.name.replace( this.filters[0], '' ); - //this.debug( i, 'fwd:', fwdName ); - bestMatch = 0; - - for( j=0; j<revList.length; j++ ){ - var rev = revList[ j ]; - revName = rev.name.replace( this.filters[1], '' ); - //this.debug( '\t ', j, 'rev:', revName ); - - if( fwd !== rev ){ - if( fwdName === revName ){ - //this.debug( '\t\t exactmatch:', fwdName, revName ); - bestIndex = j; - bestMatch = fwdName.length; - break; - } - var match = this._naiveStartingAndEndingLCS( fwdName, revName ); - currMatch = match.length; - //this.debug( '\t\t match:', match, 'currMatch:', currMatch, 'bestMatch:', bestMatch ); - if( currMatch > bestMatch ){ - bestIndex = j; - bestMatch = currMatch; - } - } - } - //this.debug( '---->', i, fwd.name, bestIndex, revList[ bestIndex ].name, bestMatch ); - - var percentage = bestMatch / ( Math.min( fwdName.length, revName.length ) ); - //this.debug( '----> %', percentage * 100 ); - - if( percentage >= this.matchPercentage ){ - var pair = this._pair( - fwdList.splice( i, 1 )[0], - revList.splice( bestIndex, 1 )[0], - { silent: true } - ); - paired.push( pair ); - if( fwdList.length <= 0 || revList.length <= 0 ){ - return paired; - } - } else { - i += 1; - } - } - //this.debug( 'remaining Forward:' ); - //this._printList( this.unpairedForward ); - //this.debug( 'remaining Reverse:' ); - //this._printList( this.unpairedReverse ); - //this.debug( '' ); - return paired; - }, + }), /** return the concat'd longest common prefix and suffix from two strings */ _naiveStartingAndEndingLCS : function( s1, s2 ){ @@ -1338,19 +1290,19 @@ // ........................................................................ paired - drag and drop re-ordering //_dragenterPairedColumns : function( ev ){ - // console.debug( '_dragenterPairedColumns:', ev ); + // this.debug( '_dragenterPairedColumns:', ev ); //}, //_dragleavePairedColumns : function( ev ){ - // //console.debug( '_dragleavePairedColumns:', ev ); + // //this.debug( '_dragleavePairedColumns:', ev ); //}, /** track the mouse drag over the paired list adding a placeholder to show where the drop would occur */ _dragoverPairedColumns : function( ev ){ - //console.debug( '_dragoverPairedColumns:', ev ); + //this.debug( '_dragoverPairedColumns:', ev ); ev.preventDefault(); var $list = this.$( '.paired-columns .column-datasets' ); this._checkForAutoscroll( $list, ev.originalEvent.clientY ); - //console.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); + //this.debug( ev.originalEvent.clientX, ev.originalEvent.clientY ); var $nearest = this._getNearestPairedDatasetLi( ev.originalEvent.clientY ); $( '.paired-drop-placeholder' ).remove(); @@ -1369,7 +1321,7 @@ scrollTop = $element.scrollTop(), upperDist = y - offset.top, lowerDist = ( offset.top + $element.outerHeight() ) - y; - //console.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); + //this.debug( '_checkForAutoscroll:', scrollTop, upperDist, lowerDist ); if( upperDist >= 0 && upperDist < this.autoscrollDist ){ $element.scrollTop( scrollTop - AUTOSCROLL_SPEED ); } else if( lowerDist >= 0 && lowerDist < this.autoscrollDist ){ @@ -1388,7 +1340,7 @@ top = $li.offset().top, halfHeight = Math.floor( $li.outerHeight() / 2 ) + WIGGLE; if( top + halfHeight > y && top - halfHeight < y ){ - //console.debug( y, top + halfHeight, top - halfHeight ) + //this.debug( y, top + halfHeight, top - halfHeight ) return $li; } } @@ -1419,13 +1371,13 @@ this.$( '.paired-columns .dataset.paired' ).each( function(){ newPaired.push( $( this ).data( 'pair' ) ); }); - //console.debug( newPaired ); + //this.debug( newPaired ); this.paired = newPaired; this._renderPaired(); }, /** drag communication with pair sub-views: dragstart */ _pairDragstart : function( ev, pair ){ - //console.debug( '_pairDragstart', ev, pair ) + //this.debug( '_pairDragstart', ev, pair ) // auto select the pair causing the event and move all selected pair.$el.addClass( 'selected' ); var $selected = this.$( '.paired-columns .dataset.selected' ); @@ -1433,7 +1385,7 @@ }, /** drag communication with pair sub-views: dragend - remove the placeholder */ _pairDragend : function( ev, pair ){ - //console.debug( '_pairDragend', ev, pair ) + //this.debug( '_pairDragend', ev, pair ) $( '.paired-drop-placeholder' ).remove(); this.$dragging = null; }, @@ -1736,7 +1688,6 @@ //============================================================================= /** a modal version of the paired collection creator */ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){ - console.log( datasets ); options = _.defaults( options || {}, { datasets : datasets, diff -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e -r 581d871b810205f6a02e994983ffe316e206b746 static/scripts/packed/mvc/collection/paired-collection-creator.js --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1,1 +1,1 @@ -define(["utils/levenshtein","utils/natural-sort","mvc/base-mvc","utils/localization"],function(h,g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(i){this.pair=i.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(i){i.currentTarget.style.opacity="0.4";if(i.originalEvent){i=i.originalEvent}i.dataTransfer.effectAllowed="move";i.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(i){i.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(i){this.$el.parent().trigger(i)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(i){i=_.defaults(i,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=i.datasets;this.historyId=i.historyId;this.filters=this.commonFilters[i.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(i.filters)){this.filters=i.filters}this.automaticallyPair=i.automaticallyPair;this.matchPercentage=i.matchPercentage;this.strategy=this.strategies[i.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(i.strategy)){this.strategy=i.strategy}this.removeExtensions=true;this.oncancel=i.oncancel;this.oncreate=i.oncreate;this.autoscrollDist=i.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(i){i.sort(function(k,j){return g(k.name,j.name)});return i},_ensureIds:function(){this.initialList.forEach(function(i){if(!i.hasOwnProperty("id")){i.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(l){var k=[],i=[];function j(m){if(this._filterFwdFn(m)){k.push(m)}if(this._filterRevFn(m)){i.push(m)}}this.unpaired.forEach(_.bind(j,this));return[k,i]},_filterFwdFn:function(j){var i=new RegExp(this.filters[0]);return i.test(j.name)},_filterRevFn:function(j){var i=new RegExp(this.filters[1]);return i.test(j.name)},_addToUnpaired:function(j){var i=function(k,m){if(k===m){return k}var l=Math.floor((m-k)/2)+k,n=g(j.name,this.unpaired[l].name);if(n<0){return i(k,l)}else{if(n>0){return i(l+1,m)}}while(this.unpaired[l]&&this.unpaired[l].name===j.name){l++}return l}.bind(this);this.unpaired.splice(i(0,this.unpaired.length),0,j)},autoPair:function(j){j=j||this.strategy;var i=this.simpleAutoPair();i=i.concat(this[j].call(this));return i},simpleAutoPair:function(){var p=0,n,t=this._splitByFilters(),k=t[0],s=t[1],r,v,l=false,u=[];while(p<k.length){var o=k[p];r=o.name.replace(this.filters[0],"");l=false;for(n=0;n<s.length;n++){var q=s[n];v=q.name.replace(this.filters[1],"");if(o!==q&&r===v){l=true;var m=this._pair(k.splice(p,1)[0],s.splice(n,1)[0],{silent:true});u.push(m);break}}if(!l){p+=1}}return u},autoPairLevenshtein:function(){var q=0,o,v=this._splitByFilters(),k=v[0],t=v[1],s,y,l,u,m,w=[];while(q<k.length){var p=k[q];s=p.name.replace(this.filters[0],"");m=Number.MAX_VALUE;for(o=0;o<t.length;o++){var r=t[o];y=r.name.replace(this.filters[1],"");if(p!==r){if(s===y){u=o;m=0;break}l=levenshteinDistance(s,y);if(l<m){u=o;m=l}}}var x=1-(m/(Math.max(s.length,y.length)));if(x>=this.matchPercentage){var n=this._pair(k.splice(q,1)[0],t.splice(u,1)[0],{silent:true});w.push(n);if(k.length<=0||t.length<=0){return w}}else{q+=1}}return w},autoPairLCSs:function(){var o=0,m,v=this._splitByFilters(),k=v[0],t=v[1],s,z,y,u,q,w=[];if(!k.length||!t.length){return w}while(o<k.length){var n=k[o];s=n.name.replace(this.filters[0],"");q=0;for(m=0;m<t.length;m++){var r=t[m];z=r.name.replace(this.filters[1],"");if(n!==r){if(s===z){u=m;q=s.length;break}var p=this._naiveStartingAndEndingLCS(s,z);y=p.length;if(y>q){u=m;q=y}}}var x=q/(Math.min(s.length,z.length));if(x>=this.matchPercentage){var l=this._pair(k.splice(o,1)[0],t.splice(u,1)[0],{silent:true});w.push(l);if(k.length<=0||t.length<=0){return w}}else{o+=1}}return w},_naiveStartingAndEndingLCS:function(n,l){var o="",p="",m=0,k=0;while(m<n.length&&m<l.length){if(n[m]!==l[m]){break}o+=n[m];m+=1}if(m===n.length){return n}if(m===l.length){return l}m=(n.length-1);k=(l.length-1);while(m>=0&&k>=0){if(n[m]!==l[k]){break}p=[n[m],p].join("");m-=1;k-=1}return o+p},_pair:function(k,i,j){j=j||{};var l=this._createPair(k,i,j.name);this.paired.push(l);this.unpaired=_.without(this.unpaired,k,i);if(!j.silent){this.trigger("pair:new",l)}return l},_createPair:function(k,i,j){if(!(k&&i)||(k===i)){throw new Error("Bad pairing: "+[JSON.stringify(k),JSON.stringify(i)])}j=j||this._guessNameForPair(k,i);return{forward:k,name:j,reverse:i}},_guessNameForPair:function(k,i,l){l=(l!==undefined)?(l):(this.removeExtensions);var j=this._naiveStartingAndEndingLCS(k.name.replace(this.filters[0],""),i.name.replace(this.filters[1],""));if(l){var m=j.lastIndexOf(".");if(m>0){j=j.slice(0,m)}}return j||(k.name+" & "+i.name)},_unpair:function(j,i){i=i||{};if(!j){throw new Error("Bad pair: "+JSON.stringify(j))}this.paired=_.without(this.paired,j);this._addToUnpaired(j.forward);this._addToUnpaired(j.reverse);if(!i.silent){this.trigger("pair:unpair",[j])}return j},unpairAll:function(){var i=[];while(this.paired.length){i.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",i)},_pairToJSON:function(i){return{collection_type:"paired",src:"new_collection",name:i.name,element_identifiers:[{name:"forward",id:i.forward.id,src:"hda"},{name:"reverse",id:i.reverse.id,src:"hda"}]}},createList:function(k){var l=this,j;if(l.historyId){j="/api/histories/"+this.historyId+"/contents/dataset_collections"}var i={type:"dataset_collection",collection_type:"list:paired",name:_.escape(k||l.$(".collection-name").val()),element_identifiers:l.paired.map(function(m){return l._pairToJSON(m)})};return jQuery.ajax(j,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(i)}).fail(function(o,m,n){l._ajaxErrHandler(o,m,n)}).done(function(m,n,o){l.trigger("collection:created",m,n,o);if(typeof l.oncreate==="function"){l.oncreate.call(this,m,n,o)}})},_ajaxErrHandler:function(l,i,k){this.error(l,i,k);var j=d("An error occurred while creating this collection");if(l){if(l.readyState===0&&l.status===0){j+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(l.responseJSON){j+="<br /><pre>"+JSON.stringify(l.responseJSON)+"</pre>"}else{j+=": 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','Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.'].join("")),"</p>","<p>",d(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','<i data-target=".remove-extensions-prompt">"Remove file extensions from pair names?"</i> control.'].join("")),"</p>","<p>",d(['Once your collection is complete, enter a <i data-target=".collection-name">name</i> and ','click <i data-target=".create-collection">"Create list"</i>. ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function i(k,j){k=k||"body";if(!this.size()){return this}$(this).each(function(){var m=$(this),l=m.data("target");if(l){m.mouseover(function(n){$(l,k).css({background:j})}).mouseout(function(n){$(l).css({background:""})})}});return this}})}());var b=function c(k,i){console.log(k);i=_.defaults(i||{},{datasets:k,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var j=new e(i).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:j.$el,width:"80%",height:"800px",closing_events:true});window.PCC=j;return j};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file +define(["utils/levenshtein","utils/natural-sort","mvc/base-mvc","utils/localization"],function(h,b,f,c){var i=Backbone.View.extend(f.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(l){this.pair=l.pair||{}},template:_.template(['<span class="forward-dataset-name flex-column"><%= pair.forward.name %></span>','<span class="pair-name-column flex-column">','<span class="pair-name"><%= pair.name %></span>',"</span>",'<span class="reverse-dataset-name flex-column"><%= pair.reverse.name %></span>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(l){l.currentTarget.style.opacity="0.4";if(l.originalEvent){l=l.originalEvent}l.dataTransfer.effectAllowed="move";l.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(l){l.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(l){this.$el.parent().trigger(l)},toString:function(){return"PairView("+this.pair.name+")"}});function g(m){m=m||{};m.createPair=m.createPair||function l(r){this.debug("creating pair:",r.listA[r.indexA].name,r.listB[r.indexB].name);r=r||{};return this._pair(r.listA.splice(r.indexA,1)[0],r.listB.splice(r.indexB,1)[0],{silent:true})};var o=[];function q(){if(!o.length){o=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]}return o}m.preprocessMatch=m.preprocessMatch||function n(s){var r=q.call(this);return _.extend(s,{matchTo:s.matchTo.name.replace(r[0],""),possible:s.possible.name.replace(r[1],"")})};return function p(t){this.debug("autopair _strategy ---------------------------");t=t||{};var r=t.listA,A=t.listB,z=0,y,v={score:0,index:null},x=[];this.debug("starting list lens:",r.length,A.length);this.debug("bestMatch (starting):",JSON.stringify(v,null," "));while(z<r.length){var w=r[z];v.score=0;for(y=0;y<A.length;y++){var u=A[y];this.debug(z+":"+w.name);this.debug(y+":"+u.name);if(r[z]!==A[y]){v=m.match.call(this,m.preprocessMatch.call(this,{matchTo:w,possible:u,index:y,bestMatch:v}));this.debug("bestMatch:",JSON.stringify(v,null," "));if(v.score===1){this.debug("breaking early due to perfect match");break}}}var s=m.scoreThreshold.call(this);this.debug("scoreThreshold:",s);this.debug("bestMatch.score:",v.score);if(v.score>=s){this.debug("creating pair");x.push(m.createPair.call(this,{listA:r,indexA:z,listB:A,indexB:v.index}));this.debug("list lens now:",r.length,A.length)}else{z+=1}if(!r.length||!A.length){return x}}this.debug("paired:",JSON.stringify(x,null," "));this.debug("autopair _strategy ---------------------------");return x}}var k=Backbone.View.extend(f.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(l){l=_.defaults(l,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,strategy:"lcs",matchPercentage:0.9,twoPassAutopairing:true});this.initialList=l.datasets;this.historyId=l.historyId;this.filters=this.commonFilters[l.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(l.filters)){this.filters=l.filters}this.automaticallyPair=l.automaticallyPair;this.strategy=this.strategies[l.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(l.strategy)){this.strategy=l.strategy}this.matchPercentage=l.matchPercentage;this.twoPassAutopairing=l.twoPassAutopairing;this.removeExtensions=true;this.oncancel=l.oncancel;this.oncreate=l.oncreate;this.autoscrollDist=l.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(l){l.sort(function(n,m){return b(n.name,m.name)});return l},_ensureIds:function(){this.initialList.forEach(function(l){if(!l.hasOwnProperty("id")){l.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(){var o=this.filters.map(function(p){return new RegExp(p)}),m=[[],[]];function n(p,q){return q.test(p.name)}this.unpaired.forEach(function l(p){o.forEach(function(r,q){if(n(p,r)){m[q].push(p)}})});return m},_addToUnpaired:function(m){var l=function(n,p){if(n===p){return n}var o=Math.floor((p-n)/2)+n,q=b(m.name,this.unpaired[o].name);if(q<0){return l(n,o)}else{if(q>0){return l(o+1,p)}}while(this.unpaired[o]&&this.unpaired[o].name===m.name){o++}return o}.bind(this);this.unpaired.splice(l(0,this.unpaired.length),0,m)},autoPair:function(n){var m=this._splitByFilters(),l=[];if(this.twoPassAutopairing){l=this.autopairSimple({listA:m[0],listB:m[1]});m=this._splitByFilters()}n=n||this.strategy;m=this._splitByFilters();l=l.concat(this[n].call(this,{listA:m[0],listB:m[1]}));return l},autopairSimple:g({scoreThreshold:function(){return 1},match:function j(l){l=l||{};if(l.matchTo===l.possible){return{index:l.index,score:1}}return l.bestMatch}}),autopairLevenshtein:g({scoreThreshold:function(){return this.matchPercentage},match:function e(m){m=m||{};var n=h(m.matchTo,m.possible),l=1-(n/(Math.max(m.matchTo.length,m.possible.length)));if(l>m.bestMatch.score){return{index:m.index,score:l}}return m.bestMatch}}),autopairLCS:g({scoreThreshold:function(){return this.matchPercentage},match:function e(n){n=n||{};var l=this._naiveStartingAndEndingLCS(n.matchTo,n.possible).length,m=l/(Math.max(n.matchTo.length,n.possible.length));if(m>n.bestMatch.score){return{index:n.index,score:m}}return n.bestMatch}}),_naiveStartingAndEndingLCS:function(o,m){var p="",q="",n=0,l=0;while(n<o.length&&n<m.length){if(o[n]!==m[n]){break}p+=o[n];n+=1}if(n===o.length){return o}if(n===m.length){return m}n=(o.length-1);l=(m.length-1);while(n>=0&&l>=0){if(o[n]!==m[l]){break}q=[o[n],q].join("");n-=1;l-=1}return p+q},_pair:function(n,l,m){m=m||{};var o=this._createPair(n,l,m.name);this.paired.push(o);this.unpaired=_.without(this.unpaired,n,l);if(!m.silent){this.trigger("pair:new",o)}return o},_createPair:function(n,l,m){if(!(n&&l)||(n===l)){throw new Error("Bad pairing: "+[JSON.stringify(n),JSON.stringify(l)])}m=m||this._guessNameForPair(n,l);return{forward:n,name:m,reverse:l}},_guessNameForPair:function(n,l,o){o=(o!==undefined)?(o):(this.removeExtensions);var m=this._naiveStartingAndEndingLCS(n.name.replace(this.filters[0],""),l.name.replace(this.filters[1],""));if(o){var p=m.lastIndexOf(".");if(p>0){m=m.slice(0,p)}}return m||(n.name+" & "+l.name)},_unpair:function(m,l){l=l||{};if(!m){throw new Error("Bad pair: "+JSON.stringify(m))}this.paired=_.without(this.paired,m);this._addToUnpaired(m.forward);this._addToUnpaired(m.reverse);if(!l.silent){this.trigger("pair:unpair",[m])}return m},unpairAll:function(){var l=[];while(this.paired.length){l.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",l)},_pairToJSON:function(l){return{collection_type:"paired",src:"new_collection",name:l.name,element_identifiers:[{name:"forward",id:l.forward.id,src:"hda"},{name:"reverse",id:l.reverse.id,src:"hda"}]}},createList:function(n){var o=this,m;if(o.historyId){m="/api/histories/"+this.historyId+"/contents/dataset_collections"}var l={type:"dataset_collection",collection_type:"list:paired",name:_.escape(n||o.$(".collection-name").val()),element_identifiers:o.paired.map(function(p){return o._pairToJSON(p)})};return jQuery.ajax(m,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(l)}).fail(function(r,p,q){o._ajaxErrHandler(r,p,q)}).done(function(p,q,r){o.trigger("collection:created",p,q,r);if(typeof o.oncreate==="function"){o.oncreate.call(this,p,q,r)}})},_ajaxErrHandler:function(o,l,n){this.error(o,l,n);var m=c("An error occurred while creating this collection");if(o){if(o.readyState===0&&o.status===0){m+=": "+c("Galaxy could not be reached and may be updating.")+c(" Try again in a few minutes.")}else{if(o.responseJSON){m+="<br /><pre>"+JSON.stringify(o.responseJSON)+"</pre>"}else{m+=": "+n}}}creator._showAlert(m,"alert-danger")},render:function(l,m){this.$el.empty().html(k.templates.main());this._renderHeader(l);this._renderMiddle(l);this._renderFooter(l);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(m,n){var l=this.$(".header").empty().html(k.templates.header()).find(".help-content").prepend($(k.templates.helpContent()));this._renderFilters();return l},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(m,n){var l=this.$(".middle").empty().html(k.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return l},_renderUnpaired:function(q,r){var o=this,p,m,l=[],n=this._splitByFilters();this.$(".forward-column .title").text([n[0].length,c("unpaired forward")].join(" "));this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[0].length));this.$(".reverse-column .title").text([n[1].length,c("unpaired reverse")].join(" "));this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-n[1].length));this.$(".unpaired-columns .column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}m=n[1].map(function(t,s){if((n[0][s]!==undefined)&&(n[0][s]!==t)){l.push(o._renderPairButton())}return o._renderUnpairedDataset(t)});p=n[0].map(function(s){return o._renderUnpairedDataset(s)});if(!p.length&&!m.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns .forward-column .column-datasets").append(p).add(this.$(".unpaired-columns .paired-column .column-datasets").append(l)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(m));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(l){return["(",l," ",c("filtered out"),")"].join("")},_renderUnpairedDataset:function(l){return $("<li/>").attr("id","dataset-"+l.id).addClass("dataset unpaired").attr("draggable",true).addClass(l.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(l.name)).data("dataset",l)},_renderPairButton:function(){return $("<li/>").addClass("dataset unpaired").append($("<span/>").addClass("dataset-name").text(c("Pair these datasets")))},_renderUnpairedEmpty:function(){var l=$('<div class="empty-message"></div>').text("("+c("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(l);return l},_renderUnpairedNotShown:function(){var l=$('<div class="empty-message"></div>').text("("+c("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(l);return l},_adjUnpairedOnScrollbar:function(){var o=this.$(".unpaired-columns").last(),p=this.$(".unpaired-columns .reverse-column .dataset").first();if(!p.size()){return}var l=o.offset().left+o.outerWidth(),n=p.offset().left+p.outerWidth(),m=Math.floor(l)-Math.floor(n);this.$(".unpaired-columns .forward-column").css("margin-left",(m>0)?m:0)},_renderPaired:function(m,n){this.$(".paired-column-title .title").text([this.paired.length,c("paired")].join(" "));this.$(".unpair-all-link").toggle(this.paired.length!==0);if(this.paired.length===0){this._renderPairedEmpty();return}else{this.$(".remove-extensions-link").show()}this.$(".paired-columns .column-datasets").empty();var l=this;this.paired.forEach(function(q,o){var p=new i({pair:q});l.$(".paired-columns .column-datasets").append(p.render().$el).append(['<button class="unpair-btn">','<span class="fa fa-unlink" title="',c("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var l=$('<div class="empty-message"></div>').text("("+c("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(l);return l},_renderFooter:function(m,n){var l=this.$(".footer").empty().html(k.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return l},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(l){function m(p,o){return['<button class="filter-choice btn" ','data-forward="',p,'" data-reverse="',o,'">',c("Forward"),": ",p,", ",c("Reverse"),": ",o,"</button>"].join("")}var n=$(_.template(['<div class="choose-filters">','<div class="help">',c("Choose from the following filters to change which unpaired reads are shown in the display"),":</div>",m("_1","_2"),m("_R1","_R2"),"</div>"].join(""))({}));return this.$(l).popover({container:".collection-creator",placement:"bottom",html:true,content:n})},_validationWarning:function(m,l){var n="validation-warning";if(m==="name"){m=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(l){m=m||this.$("."+n);m.removeClass(n)}else{m.addClass(n)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(l){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter input").val(),this.$(".reverse-unpaired-filter input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var l,m=null;if(this.paired.length){m="alert-success";l=this.paired.length+" "+c("pairs created");if(!this.unpaired.length){l+=": "+c("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{l=c("Could not automatically create any pairs from the given dataset names")}this._showAlert(l,m)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(l){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(l){$(l.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter input":function(l){this.trigger("filter-change")},"focus .reverse-unpaired-filter input":function(l){$(l.currentTarget).select()},"click .forward-column .dataset.unpaired":"_clickUnpairedDataset","click .reverse-column .dataset.unpaired":"_clickUnpairedDataset","click .paired-column .dataset.unpaired":"_clickPairRow","click .unpaired-columns":"clearSelectedUnpaired","mousedown .unpaired-columns .dataset":"_mousedownUnpaired","click .paired-column-title":"_clickShowOnlyPaired","mousedown .flexible-partition-drag":"_startPartitionDrag","click .paired-columns .dataset.paired":"selectPair","click .paired-columns":"clearSelectedPaired","click .paired-columns .pair-name":"_clickPairName","click .unpair-btn":"_clickUnpair","dragover .paired-columns .column-datasets":"_dragoverPairedColumns","drop .paired-columns .column-datasets":"_dropPairedColumns","pair.dragstart .paired-columns .column-datasets":"_pairDragstart","pair.dragend .paired-columns .column-datasets":"_pairDragend","change .remove-extensions":function(l){this.toggleExtensions()},"change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(l){if(typeof this.oncancel==="function"){this.oncancel.call(this)}},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(l){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(l){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(m,l){l=l||"alert-danger";this.$(".main-help").hide();this.$(".header .alert").attr("class","alert alert-dismissable").addClass(l).show().find(".alert-message").html(m)},_hideAlert:function(l){this.$(".main-help").show();this.$(".header .alert").hide()},_clickShowOnlyUnpaired:function(l){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(l){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(l,m){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(l,m)},hidePaired:function(l,m){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(l,m)},splitView:function(l,m){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(l,m);return this},_clickUnpairAll:function(l){this.unpairAll()},_clickAutopair:function(l){this.autoPair();this.trigger("autopair")},_clickFilterChoice:function(m){var l=$(m.currentTarget);this.$(".forward-unpaired-filter input").val(l.data("forward"));this.$(".reverse-unpaired-filter input").val(l.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(l){this.$(".forward-unpaired-filter input").val("");this.$(".reverse-unpaired-filter input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(l){l.stopPropagation();return this.toggleSelectUnpaired($(l.currentTarget))},toggleSelectUnpaired:function(n,m){m=m||{};var o=n.data("dataset"),l=m.force!==undefined?m.force:!n.hasClass("selected");if(!n.size()||o===undefined){return n}if(l){n.addClass("selected");if(!m.waitToPair){this.pairAllSelected()}}else{n.removeClass("selected")}return n},pairAllSelected:function(m){m=m||{};var n=this,o=[],l=[],p=[];n.$(".unpaired-columns .forward-column .dataset.selected").each(function(){o.push($(this).data("dataset"))});n.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){l.push($(this).data("dataset"))});o.length=l.length=Math.min(o.length,l.length);o.forEach(function(r,q){try{p.push(n._pair(r,l[q],{silent:true}))}catch(s){n.error(s)}});if(p.length&&!m.silent){this.trigger("pair:new",p)}return p},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(n){if(n.shiftKey){var m=this,l=$(n.target).addClass("selected"),o=function(p){m.$(p.target).filter(".dataset").addClass("selected")};l.parent().on("mousemove",o);$(document).one("mouseup",function(p){l.parent().off("mousemove",o);m.pairAllSelected()})}},_clickPairRow:function(n){var o=$(n.currentTarget).index(),m=$(".unpaired-columns .forward-column .dataset").eq(o).data("dataset"),l=$(".unpaired-columns .reverse-column .dataset").eq(o).data("dataset");this._pair(m,l)},_startPartitionDrag:function(m){var l=this,p=m.pageY;$("body").css("cursor","ns-resize");l.$(".flexible-partition-drag").css("color","black");function o(q){l.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",n)}function n(q){var r=q.pageY-p;if(!l.adjPartition(r)){$("body").trigger("mouseup")}l._adjUnpairedOnScrollbar();p+=r}$("body").mousemove(n);$("body").one("mouseup",o)},adjPartition:function(m){var l=this.$(".unpaired-columns"),n=this.$(".paired-columns"),o=parseInt(l.css("height"),10),p=parseInt(n.css("height"),10);o=Math.max(10,o+m);p=p-m;var q=m<0;if(q){if(this.unpairedPanelHidden){return false}else{if(o<=10){this.hideUnpaired();return false}}}else{if(this.unpairedPanelHidden){l.show();this.unpairedPanelHidden=false}}if(!q){if(this.pairedPanelHidden){return false}else{if(p<=15){this.hidePaired();return false}}}else{if(this.pairedPanelHidden){n.show();this.pairedPanelHidden=false}}l.css({height:o+"px",flex:"0 0 auto"});return true},selectPair:function(l){l.stopPropagation();$(l.currentTarget).toggleClass("selected")},clearSelectedPaired:function(l){this.$(".paired-columns .dataset.selected").removeClass("selected")},_clickPairName:function(o){o.stopPropagation();var q=$(o.currentTarget),n=q.parent().parent(),m=n.index(".dataset.paired"),p=this.paired[m],l=prompt("Enter a new name for the pair:",p.name);if(l){p.name=l;p.customizedName=true;q.text(p.name)}},_clickUnpair:function(m){var l=Math.floor($(m.currentTarget).index(".unpair-btn"));this._unpair(this.paired[l])},_dragoverPairedColumns:function(o){o.preventDefault();var m=this.$(".paired-columns .column-datasets");this._checkForAutoscroll(m,o.originalEvent.clientY);var n=this._getNearestPairedDatasetLi(o.originalEvent.clientY);$(".paired-drop-placeholder").remove();var l=$('<div class="paired-drop-placeholder"></div>');if(!n.size()){m.append(l)}else{n.before(l)}},_checkForAutoscroll:function(l,r){var p=2;var 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',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"</p>"].join(""))};(function(){jQuery.fn.extend({hoverhighlight:function l(n,m){n=n||"body";if(!this.size()){return this}$(this).each(function(){var p=$(this),o=p.data("target");if(o){p.mouseover(function(q){$(o,n).css({background:m})}).mouseout(function(q){$(o).css({background:""})})}});return this}})}());var d=function a(n,l){l=_.defaults(l||{},{datasets:n,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var m=new k(l).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:m.$el,width:"80%",height:"800px",closing_events:true});window.PCC=m;return m};return{PairedCollectionCreator:k,pairedCollectionCreatorModal:d}}); \ No newline at end of file diff -r cd41c43e857f7db0d21a093f0d59ce8bf82a049e -r 581d871b810205f6a02e994983ffe316e206b746 test/qunit/tests/paired-collection-creator.js --- a/test/qunit/tests/paired-collection-creator.js +++ b/test/qunit/tests/paired-collection-creator.js @@ -22,7 +22,7 @@ ok( pcc.hasOwnProperty( 'options' ) && typeof pcc.options === 'object' ); deepEqual( pcc.options.filters, pcc.DEFAULT_FILTERS ); ok( pcc.options.automaticallyPair ); - equal( pcc.options.matchPercentage, 1.0 ); + equal( pcc.options.matchPercentage, 0.9 ); equal( pcc.options.strategy, 'lcs' ); }); @@ -44,6 +44,36 @@ equal( pcc.paired.length, pcc.initialList.length / 2 ); }); + test( "Try easy autopairing with simple exact matching", function() { + var pcc = new PCC({ + datasets : DATA._1, + strategy : 'simple', + twoPassAutopairing : false + }); + equal( pcc.unpaired.length, 0 ); + equal( pcc.paired.length, pcc.initialList.length / 2 ); + }); + + test( "Try easy autopairing with LCS", function() { + var pcc = new PCC({ + datasets : DATA._1, + strategy : 'lcs', + twoPassAutopairing : false + }); + equal( pcc.unpaired.length, 0 ); + equal( pcc.paired.length, pcc.initialList.length / 2 ); + }); + + test( "Try easy autopairing with Levenshtein", function() { + var pcc = new PCC({ + datasets : DATA._1, + strategy : 'levenshtein', + twoPassAutopairing : false + }); + equal( pcc.unpaired.length, 0 ); + equal( pcc.paired.length, pcc.initialList.length / 2 ); + }); + //TODO: // filters: clearing, setting via popover, regex // partition: maximize paired, maximize unpaired, split evenly @@ -69,10 +99,9 @@ ); }); - console.debug( 'requestBody:', JSON.stringify( requestJSON, null, ' ' ) ); + //console.debug( 'requestBody:', JSON.stringify( requestJSON, null, ' ' ) ); pcc.createList( 'Heres a collection' ); server.respond(); deepEqual( requestJSON, DATA._1requestJSON ); }); - }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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