[galaxy-commits] commit/galaxy-central: carlfeberhard: Paired collections: prototype creator modal (accessible from the multi-select commands) allowing the user to create a paired collection

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4d11f590b0a4/ Changeset: 4d11f590b0a4 User: carlfeberhard Date: 2014-06-18 15:56:29 Summary: Paired collections: prototype creator modal (accessible from the multi-select commands) allowing the user to create a paired collection Affected #: 6 files diff -r e8c791f71470aed7da9c3418f2f7cc754dff1fd6 -r 4d11f590b0a4389f6d9e5b30573acdcbc07e4fe6 static/scripts/mvc/collection/paired-collection-creator.js --- /dev/null +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -0,0 +1,1485 @@ +define([ + "mvc/base-mvc", + "utils/localization" +], function( baseMVC, _l ){ +//============================================================================= +/** An interface for building collections of paired datasets. + */ +var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).extend({ + + /** set up initial options, instance vars, behaviors, and autopair (if set to do so) */ + initialize : function( attributes ){ + //console.debug( '-- PairedCollectionCreator:', attributes ); + + attributes = _.defaults( attributes, { + datasets : [], + filters : this.DEFAULT_FILTERS, + automaticallyPair : true, + matchPercentage : 1.0, + //matchPercentage : 0.9, + //matchPercentage : 0.8, + //strategy : 'levenshtein' + strategy : 'lcs' + }); + //console.debug( 'attributes now:', attributes ); + + /** unordered, original list */ + this.initialList = attributes.datasets; + + /** is this from a history? if so, what's its id? */ + this.historyId = attributes.historyId; + + /** which filters should be used initially? (String[2] or name in commonFilters) */ + this.filters = this.commonFilters[ attributes.filters ] || this.commonFilters[ this.DEFAULT_FILTERS ]; + if( _.isArray( attributes.filters ) ){ + this.filters = attributes.filters; + } + + /** 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; + } + + /** fn to call when the cancel button is clicked (scoped to this) - if falsy, no btn is displayed */ + this.oncancel = attributes.oncancel; + /** fn to call when the collection is created (scoped to this) */ + this.oncreate = attributes.oncreate; + + /** is the unpaired panel shown? */ + this.unpairedPanelHidden = false; + /** is the paired panel shown? */ + this.pairedPanelHidden = false; + + this._dataSetUp(); + + this._setUpBehaviors(); + }, + + /** map of common filter pairs by name */ + commonFilters : { + none : [ '', '' ], + illumina : [ '_1', '_2' ] + }, + /** which commonFilter to use by default */ + DEFAULT_FILTERS : 'illumina', + //DEFAULT_FILTERS : 'none', + + /** map of name->fn for autopairing */ + strategies : { + 'lcs' : 'autoPairLCSs', + 'levenshtein' : 'autoPairLevenshtein' + }, + /** default autopair strategy name */ + DEFAULT_STRATEGY : 'lcs', + + // ------------------------------------------------------------------------ process raw list + /** set up main data: cache initialList, sort, and autopair */ + _dataSetUp : function(){ + //console.debug( '-- _dataSetUp' ); + + this.paired = []; + this.unpaired = []; + + //this.fwdSelectedIds = []; + //this.revSelectedIds = []; + this.selectedIds = []; + + // sort initial list, add ids if needed, and save new working copy to unpaired + this._sortInitialList(); + this._ensureIds(); + this.unpaired = this.initialList.slice( 0 ); + + if( this.automaticallyPair ){ + this.autoPair(); + } + }, + + /** sort initial list */ + _sortInitialList : function(){ + //console.debug( '-- _sortInitialList' ); + this._sortDatasetList( this.initialList ); + //this._printList( this.unpaired ); + }, + + /** sort a list of datasets */ + _sortDatasetList : function( list ){ + // currently only natural sort by name + list.sort( function( a, b ){ return naturalSort( a.name, b.name ); }); + return list; + }, + + /** add ids to dataset objs in initial list if none */ + _ensureIds : function(){ + this.initialList.forEach( function( dataset ){ + if( !dataset.hasOwnProperty( 'id' ) ){ + 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 = []; + this.unpaired.forEach( function( unpaired ){ + if( this._filterFwdFn( unpaired ) ){ + fwd.push( unpaired ); + } + if( this._filterRevFn( unpaired ) ){ + rev.push( unpaired ); + } + }.bind( this ) ); + return [ fwd, rev ]; + }, + + /** filter fn to apply to forward datasets */ + _filterFwdFn : function( dataset ){ + // simple contains for now - add more when new feat. are added (regex, etc.) + return dataset.name.indexOf( this.filters[0] ) >= 0; + }, + + /** filter fn to apply to reverse datasets */ + _filterRevFn : function( dataset ){ + return dataset.name.indexOf( this.filters[1] ) >= 0; + }, + + /** add a dataset to the unpaired list in it's proper order */ + _addToUnpaired : function( dataset ){ + // currently, unpaired is natural sorted by name, use binary search to find insertion point + var binSearchSortedIndex = function( low, hi ){ + if( low === hi ){ return low; } + + var mid = Math.floor( ( hi - low ) / 2 ) + low, + compared = naturalSort( dataset.name, this.unpaired[ mid ].name ); + + if( compared < 0 ){ + return binSearchSortedIndex( low, mid ); + } else if( compared > 0 ){ + return binSearchSortedIndex( mid + 1, hi ); + } + // walk the equal to find the last + while( this.unpaired[ mid ] && this.unpaired[ mid ].name === dataset.name ){ mid++; } + return mid; + + }.bind( this ); + + this.unpaired.splice( binSearchSortedIndex( 0, this.unpaired.length ), 0, dataset ); + }, + + // ------------------------------------------------------------------------ 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 ){ + strategy = strategy || this.strategy; + //console.debug( '-- autoPair', strategy ); + this.simpleAutoPair(); + return this[ strategy ].call( this ); + }, + + /** attempts to pair forward with reverse when names exactly match (after removing filters) */ + simpleAutoPair : function(){ + //console.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; + + while( i<fwdList.length ){ + var fwd = fwdList[ i ]; + //TODO: go through the filterFwdFn + fwdName = fwd.name.replace( this.filters[0], '' ); + //console.debug( i, 'fwd:', fwdName ); + matchFound = false; + + for( j=0; j<revList.length; j++ ){ + var rev = revList[ j ]; + revName = rev.name.replace( this.filters[1], '' ); + //console.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 + //console.debug( '---->', fwdName, revName ); + this._pair( + fwdList.splice( i, 1 )[0], + revList.splice( j, 1 )[0], + { silent: true } + ); + break; + } + } + if( !matchFound ){ i += 1; } + } + //console.debug( 'remaining Forward:' ); + //this._printList( this.unpairedForward ); + //console.debug( 'remaining Reverse:' ); + //this._printList( this.unpairedReverse ); + //console.debug( '' ); + }, + + /** 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 + //console.debug( '-- autoPairLevenshtein' ); + var i = 0, j, + split = this._splitByFilters(), + fwdList = split[0], + revList = split[1], + fwdName, revName, + distance, bestIndex, bestDist; + + while( i<fwdList.length ){ + var fwd = fwdList[ i ]; + //TODO: go through the filterFwdFn + fwdName = fwd.name.replace( this.filters[0], '' ); + //console.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], '' ); + //console.debug( '\t ', j, 'rev:', revName ); + + if( fwd !== rev ){ + if( fwdName === revName ){ + //console.debug( '\t\t exactmatch:', fwdName, revName ); + bestIndex = j; + bestDist = 0; + break; + } + distance = levenshteinDistance( fwdName, revName ); + //console.debug( '\t\t distance:', distance, 'bestDist:', bestDist ); + if( distance < bestDist ){ + bestIndex = j; + bestDist = distance; + } + } + } + //console.debug( '---->', fwd.name, bestIndex, bestDist ); + //console.debug( '---->', fwd.name, revList[ bestIndex ].name, bestDist ); + + var percentage = 1.0 - ( bestDist / ( Math.max( fwdName.length, revName.length ) ) ); + //console.debug( '----> %', percentage * 100 ); + + if( percentage >= this.matchPercentage ){ + this._pair( + fwdList.splice( i, 1 )[0], + revList.splice( bestIndex, 1 )[0], + { silent: true } + ); + if( fwdList.length <= 0 || revList.length <= 0 ){ + return; + } + } else { + i += 1; + } + } + //console.debug( 'remaining Forward:' ); + //this._printList( this.unpairedForward ); + //console.debug( 'remaining Reverse:' ); + //this._printList( this.unpairedReverse ); + //console.debug( '' ); + }, + + /** 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 + //console.debug( '-- autoPairLCSs' ); + var i = 0, j, + split = this._splitByFilters(), + fwdList = split[0], + revList = split[1], + fwdName, revName, + currMatch, bestIndex, bestMatch; + if( !fwdList.length || !revList.length ){ return; } + //console.debug( fwdList, revList ); + + while( i<fwdList.length ){ + var fwd = fwdList[ i ]; + fwdName = fwd.name.replace( this.filters[0], '' ); + //console.debug( i, 'fwd:', fwdName ); + bestMatch = 0; + + for( j=0; j<revList.length; j++ ){ + var rev = revList[ j ]; + revName = rev.name.replace( this.filters[1], '' ); + //console.debug( '\t ', j, 'rev:', revName ); + + if( fwd !== rev ){ + if( fwdName === revName ){ + //console.debug( '\t\t exactmatch:', fwdName, revName ); + bestIndex = j; + bestMatch = fwdName.length; + break; + } + var match = this._naiveStartingAndEndingLCS( fwdName, revName ); + currMatch = match.length; + //console.debug( '\t\t match:', match, 'currMatch:', currMatch, 'bestMatch:', bestMatch ); + if( currMatch > bestMatch ){ + bestIndex = j; + bestMatch = currMatch; + } + } + } + //console.debug( '---->', i, fwd.name, bestIndex, revList[ bestIndex ].name, bestMatch ); + + var percentage = bestMatch / ( Math.min( fwdName.length, revName.length ) ); + //console.debug( '----> %', percentage * 100 ); + + if( percentage >= this.matchPercentage ){ + this._pair( + fwdList.splice( i, 1 )[0], + revList.splice( bestIndex, 1 )[0], + { silent: true } + ); + if( fwdList.length <= 0 || revList.length <= 0 ){ + return; + } + } else { + i += 1; + } + } + //console.debug( 'remaining Forward:' ); + //this._printList( this.unpairedForward ); + //console.debug( 'remaining Reverse:' ); + //this._printList( this.unpairedReverse ); + //console.debug( '' ); + }, + + /** return the concat'd longest common prefix and suffix from two strings */ + _naiveStartingAndEndingLCS : function( s1, s2 ){ + var fwdLCS = '', + revLCS = '', + i = 0, j = 0; + while( i < s1.length && i < s2.length ){ + if( s1[ i ] !== s2[ i ] ){ + break; + } + fwdLCS += s1[ i ]; + i += 1; + } + if( i === s1.length ){ return s1; } + if( i === s2.length ){ return s2; } + + i = ( s1.length - 1 ); + j = ( s2.length - 1 ); + while( i >= 0 && j >= 0 ){ + if( s1[ i ] !== s2[ j ] ){ + break; + } + revLCS = [ s1[ i ], revLCS ].join( '' ); + i -= 1; + j -= 1; + } + return fwdLCS + revLCS; + }, + + // ------------------------------------------------------------------------ pairing / unpairing + /** create a pair from fwd and rev, removing them from unpaired, and placing the new pair in paired */ + _pair : function( fwd, rev, options ){ + options = options || {}; + //TODO: eventing, options + //console.debug( '_pair:', fwd, rev ); + var pair = this._createPair( fwd, rev, options.name ); + this.paired.push( pair ); + this.unpaired = _.without( this.unpaired, fwd, rev ); + if( !options.silent ){ + this.trigger( 'pair:new', pair ); + } + return pair; + }, + + /** create a pair Object from fwd and rev, adding the name attribute (will guess if not given) */ + _createPair : function( fwd, rev, name ){ + // ensure existance and don't pair something with itself + if( !( fwd && rev ) || ( fwd === rev ) ){ + throw new Error( 'Bad pairing: ' + [ JSON.stringify( fwd ), JSON.stringify( rev ) ] ); + } + name = name || this._guessNameForPair( fwd, rev ); + return { forward : fwd, name : name, reverse : rev }; + }, + + /** try to find a good pair name for the given fwd and rev datasets */ + _guessNameForPair : function( fwd, rev ){ + var lcs = this._naiveStartingAndEndingLCS( + fwd.name.replace( this.filters[0], '' ), + rev.name.replace( this.filters[1], '' ) + ); + //TODO: optionally remove extension + return lcs || ( fwd.name + ' & ' + rev.name ); + }, + + ///** find datasets with fwdId and revID and pair them */ + //_pairById : function( fwdId, revId, name ){ + // var both = this.unpaired.filter( function( unpaired ){ + // return unpaired.id === fwdId || unpaired.id === revId; + // }), + // fwd = both[0], rev = both[1]; + // if( both[0].id === revId ){ + // fwd = rev; rev = both[0]; + // } + // return this._pair( fwd, rev, name ); + //}, + + /** unpair a pair, removing it from paired, and adding the fwd,rev datasets back into unpaired */ + _unpair : function( pair, options ){ + options = options || {}; + if( !pair ){ + throw new Error( 'Bad pair: ' + JSON.stringify( pair ) ); + } + this.paired = _.without( this.paired, pair ); + this._addToUnpaired( pair.forward ); + this._addToUnpaired( pair.reverse ); + + if( !options.silent ){ + this.trigger( 'pair:unpair', [ pair ] ); + } + return pair; + }, + + /** unpair all paired datasets */ + unpairAll : function(){ + var pairs = []; + while( this.paired.length ){ + pairs.push( this._unpair( this.paired[ 0 ], { silent: true }) ); + } + this.trigger( 'pair:unpair', pairs ); + }, + + // ------------------------------------------------------------------------ API + /** convert a pair into JSON compatible with the collections API */ + _pairToJSON : function( pair ){ + //TODO: consider making this the pair structure when created instead + return { + collection_type : 'paired', + src : 'new_collection', + name : pair.name, + element_identifiers : [{ + name : 'forward', + id : pair.forward.id, + //TODO: isn't necessarily true + src : 'hda' + }, { + name : 'reverse', + id : pair.reverse.id, + //TODO: isn't necessarily true + src : 'hda' + }] + }; + }, + + /** create the collection via the API + * @returns {jQuery.xhr Object} the jquery ajax request + */ + createList : function(){ + var creator = this, + url; + if( creator.historyId ){ + url = '/api/histories/' + this.historyId + '/contents/dataset_collections'; + //} else { + // + } + + //var xhr = jQuery.ajax({ + var ajaxData = { + type : 'dataset_collection', + collection_type : 'list:paired', + name : _.escape( creator.$( '.collection-name' ).val() ), + element_identifiers : creator.paired.map( function( pair ){ + return creator._pairToJSON( pair ); + }) + }; + url = 'blarg'; + //console.debug( JSON.stringify( ajaxData ) ); + return jQuery.ajax( url, { + type : 'POST', + contentType : 'application/json', + data : JSON.stringify( ajaxData ) + }) + .fail( function( xhr, status, message ){ + //TODO: extract method + console.error( xhr, status, message ); + var content = _l( 'An error occurred while creating this collection' ); + if( xhr ){ + if( xhr.readyState === 0 && xhr.status === 0 ){ + content += ': ' + _l( 'Galaxy could not be reached and may be updating.' ) + + _l( ' Try again in a few minutes.' ); + } else if( xhr.responseJSON ){ + content += '<br /><pre>' + JSON.stringify( xhr.responseJSON ) + '</pre>'; + } else { + content += ': ' + message; + } + } + creator._showAlert( content, 'alert-danger' ); + }) + .done( function( response, message, xhr ){ + //console.info( 'ok', response, message, xhr ); + creator.trigger( 'collection:created', response, message, xhr ); + if( typeof creator.oncreate === 'function' ){ + creator.oncreate.call( this, x, y, z ); + } + }); + }, + + // ------------------------------------------------------------------------ rendering + /** render the entire interface */ + render : function( speed, callback ){ + //console.debug( '-- _render' ); + this.$el.empty().addClass( 'collection-creator' ).html( PairedCollectionCreator.templates.main() ); + this._renderHeader( speed ); + this._renderMiddle( speed ); + this._renderFooter( speed ); + this._addPluginComponents(); + return this; + }, + + /** render the header section */ + _renderHeader : function( speed, callback ){ + //console.debug( '-- _renderHeader' ); + var $header = this.$( '.header' ).empty().html( PairedCollectionCreator.templates.header() ) + .find( '.help-content' ).prepend( $( PairedCollectionCreator.templates.helpContent() ) ); + + this._renderFilters(); + return $header; + }, + /** fill the filter inputs with the filter values */ + _renderFilters : function(){ + return this.$( '.forward-column .column-header input' ).val( this.filters[0] ) + .add( this.$( '.reverse-column .column-header input' ).val( this.filters[1] ) ); + }, + + /** render the middle including unpaired and paired sections (which may be hidden) */ + _renderMiddle : function( speed, callback ){ + var $middle = this.$( '.middle' ).empty().html( PairedCollectionCreator.templates.middle() ); + //TODO: use replaceWith + if( this.unpairedPanelHidden ){ + this.$( '.unpaired-columns' ).hide(); + } else if( this.pairedPanelHidden ){ + this.$( '.paired-columns' ).hide(); + } + this._renderUnpaired(); + this._renderPaired(); + return $middle; + }, + /** render the unpaired section, showing datasets accrd. to filters, update the unpaired counts */ + _renderUnpaired : function( speed, callback ){ + //console.debug( '-- _renderUnpaired' ); + var creator = this, + $fwd, $rev, $prd = [], + split = this._splitByFilters(); + // update unpaired counts + this.$( '.forward-column .title' ) + .text([ split[0].length, _l( 'unpaired forward' ) ].join( ' ' )); + this.$( '.forward-column .unpaired-info' ) + .text( this._renderUnpairedDisplayStr( this.unpaired.length - split[0].length ) ); + this.$( '.reverse-column .title' ) + .text([ split[1].length, _l( 'unpaired reverse' ) ].join( ' ' )); + this.$( '.reverse-column .unpaired-info' ) + .text( this._renderUnpairedDisplayStr( this.unpaired.length - split[1].length ) ); + + // show/hide the auto pair button if any unpaired are left + this.$( '.autopair-link' ).toggle( this.unpaired.length !== 0 ); + if( this.unpaired.length === 0 ){ + this._renderUnpairedEmpty(); + //TODO: would be best to return here (the $columns) + } + + // create the dataset dom arrays + $rev = split[1].map( function( dataset, i ){ + // if there'll be a fwd dataset across the way, add a button to pair the row + if( ( split[0][ i ] !== undefined ) + && ( split[0][ i ] !== dataset ) ){ + $prd.push( creator._renderPairButton() ); + } + return creator._renderUnpairedDataset( dataset ); + }); + $fwd = split[0].map( function( dataset ){ + return creator._renderUnpairedDataset( dataset ); + }); + // add to appropo cols + //TODO: not the best way to render + this.$( '.unpaired-columns .column-datasets' ).empty(); + return this.$( '.unpaired-columns .forward-column .column-datasets' ).append( $fwd ) + .add( this.$( '.unpaired-columns .paired-column .column-datasets' ).append( $prd ) ) + .add( this.$( '.unpaired-columns .reverse-column .column-datasets' ).append( $rev ) ); + }, + /** return a string to display the count of filtered out datasets */ + _renderUnpairedDisplayStr : function( numFiltered ){ + return [ '(', numFiltered, ' ', _l( 'filtered out' ), ')' ].join(''); + }, + /** return an unattached jQuery DOM element to represent an unpaired dataset */ + _renderUnpairedDataset : function( dataset ){ + //TODO: to underscore template + return $( '<li/>') + .attr( 'id', 'dataset-' + dataset.id ) + .addClass( 'dataset unpaired' ) + .attr( 'draggable', true ) + .addClass( dataset.selected? 'selected': '' ) + .append( $( '<span/>' ).addClass( 'dataset-name' ).text( dataset.name ) ) + //?? + .data( 'dataset', dataset ); + }, + /** render the button that may go between unpaired datasets, allowing the user to pair a row */ + _renderPairButton : function(){ + //TODO: *not* a dataset - don't pretend like it is + return $( '<li/>').addClass( 'dataset unpaired' ) + .append( $( '<span/>' ).addClass( 'dataset-name' ).text( _l( 'Pair these datasets' ) ) ); + }, + /** a message to display when no unpaired left */ + _renderUnpairedEmpty : function(){ + //console.debug( '-- renderUnpairedEmpty' ); + var $msg = $( '<div class="empty-message"></div>' ) + .text( '(' + _l( 'no remaining unpaired datasets' ) + ')' ); + this.$( '.unpaired-columns .paired-column .column-datasets' ).prepend( $msg ); + return $msg; + }, + + /** render the paired section and update counts of paired datasets */ + _renderPaired : function( speed, callback ){ + //console.debug( '-- _renderPaired' ); + var $fwd = [], + $prd = [], + $rev = []; + + this.$( '.paired-column-title .title' ).text([ this.paired.length, _l( 'paired' ) ].join( ' ' ) ); + // show/hide the unpair all link + this.$( '.unpair-all-link' ).toggle( this.paired.length !== 0 ); + if( this.paired.length === 0 ){ + this._renderPairedEmpty(); + //TODO: would be best to return here (the $columns) + } + + this.paired.forEach( function( pair, i ){ + $fwd.push( $( '<li/>').addClass( 'dataset paired' ) + .append( $( '<span/>' ).addClass( 'dataset-name' ).text( pair.forward.name ) ) ); + $prd.push( $( '<li/>').addClass( 'dataset paired' ) + .append( $( '<span/>' ).addClass( 'dataset-name' ).text( pair.name ) ) ); + $rev.push( $( '<li/>').addClass( 'dataset paired' ) + .append( $( '<span/>' ).addClass( 'dataset-name' ).text( pair.reverse.name ) ) ); + $rev.push( $( '<button/>' ).addClass( 'unpair-btn' ) + .append( $( '<span/>' ).addClass( 'fa fa-unlink' ).attr( 'title', _l( 'Unpair' ) ) ) ); + }); + + //TODO: better as one swell foop (instead of 4 repaints) + this.$( '.paired-columns .column-datasets' ).empty(); + return this.$( '.paired-columns .forward-column .column-datasets' ).prepend( $fwd ) + .add( this.$( '.paired-columns .paired-column .column-datasets' ).prepend( $prd ) ) + .add( this.$( '.paired-columns .reverse-column .column-datasets' ).prepend( $rev ) ); + }, + /** a message to display when none paired */ + _renderPairedEmpty : function(){ + var $msg = $( '<div class="empty-message"></div>' ) + .text( '(' + _l( 'no paired datasets yet' ) + ')' ); + this.$( '.paired-columns .paired-column .column-datasets' ).prepend( $msg ); + return $msg; + }, + + /** render the footer, completion controls, and cancel controls */ + _renderFooter : function( speed, callback ){ + var $footer = this.$( '.footer' ).empty().html( PairedCollectionCreator.templates.footer() ); + if( typeof this.oncancel === 'function' ){ + this.$( '.cancel-create.btn' ).show(); + } + return $footer; + }, + + /** add any jQuery/bootstrap/custom plugins to elements rendered */ + _addPluginComponents : function(){ + this._chooseFiltersPopover( '.choose-filters-link' ); + this.$( '.help-content i' ).hoverhighlight( '.collection-creator', 'rgba( 192, 255, 255, 1.0 )' ); + }, + + /** build a filter selection popover allowing selection of common filter pairs */ + _chooseFiltersPopover : function( selector ){ + function filterChoice( val1, val2 ){ + return [ + '<button class="filter-choice btn" ', + 'data-forward="', val1, '" data-reverse="', val2, '">', + _l( 'Forward' ), ': ', val1, ', ', + _l( 'Reverse' ), ': ', val2, + '</button>' + ].join(''); + } + var $popoverContent = $( _.template([ + '<div class="choose-filters">', + '<div class="help">', + _l( 'Choose from the following filters to change which unpaired reads are shown in the display' ), + ':</div>', + //TODO: connect with common filters + filterChoice( '_1', '_2' ), + filterChoice( '_R1', '_R2' ), + '</div>' + ].join(''), {})); + + return this.$( selector ).popover({ + container : '.collection-creator', + placement : 'bottom', + html : true, + //animation : false, + content : $popoverContent + }); + }, + + /** add (or clear if clear is truthy) a validation warning to what */ + _validationWarning : function( what, clear ){ + var VALIDATION_CLASS = 'validation-warning'; + if( what === 'name' ){ + what = this.$( '.collection-name' ).add( this.$( '.collection-name-prompt' ) ); + this.$( '.collection-name' ).focus().select(); + } + if( clear ){ + what = what || this.$( '.' + VALIDATION_CLASS ); + what.removeClass( VALIDATION_CLASS ); + } else { + what.addClass( VALIDATION_CLASS ); + } + }, + + // ------------------------------------------------------------------------ events + /** set up event handlers on self */ + _setUpBehaviors : function(){ + this.on( 'pair:new', function(){ + //TODO: ideally only re-render the columns (or even elements) involved + this._renderUnpaired(); + this._renderPaired(); + + // scroll to bottom where new pairs are added + //TODO: this doesn't seem to work - innerHeight sticks at 133... + // may have to do with improper flex columns + //var $pairedView = this.$( '.paired-columns' ); + //$pairedView.scrollTop( $pairedView.innerHeight() ); + //console.debug( $pairedView.height() ) + this.$( '.paired-columns' ).scrollTop( 8000000 ); + }); + this.on( 'pair:unpair', function( pairs ){ + //TODO: ideally only re-render the columns (or even elements) involved + this._renderUnpaired(); + this._renderPaired(); + }); + + 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(); + }); + + //this.on( 'all', function(){ + // console.info( arguments ); + //}); + return this; + }, + + events : { + // header + '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', + //TODO: this seems kinda backasswards + 'change .forward-unpaired-filter input' : function( ev ){ this.trigger( 'filter-change' ); }, + 'focus .forward-unpaired-filter input' : function( ev ){ $( ev.currentTarget ).select(); }, + 'click .autopair-link' : '_clickAutopair', + 'click .choose-filters .filter-choice' : '_clickFilterChoice', + 'click .clear-filters-link' : '_clearFilters', + 'change .reverse-unpaired-filter input' : function( ev ){ this.trigger( 'filter-change' ); }, + 'focus .reverse-unpaired-filter input' : function( ev ){ $( ev.currentTarget ).select(); }, + // unpaired + 'click .forward-column .dataset.unpaired' : '_clickUnpairedDataset', + 'click .reverse-column .dataset.unpaired' : '_clickUnpairedDataset', + 'click .paired-column .dataset.unpaired' : '_clickPairRow', + 'click .unpaired-columns' : 'clearSelectedUnpaired', + // divider + 'click .paired-column-title' : '_clickShowOnlyPaired', + 'mousedown .flexible-partition-drag' : '_startPartitionDrag', + // paired + 'click .paired-columns .paired-column .dataset-name' : '_clickPairName', + 'click .unpair-btn' : '_clickUnpair', + + 'mouseover .dataset.paired' : '_hoverPaired', + 'mouseout .dataset.paired' : '_hoverOutPaired', + + // footer + 'change .collection-name' : '_changeName', + 'click .cancel-create' : function( ev ){ + if( typeof this.oncancel === 'function' ){ + this.oncancel.call( this ); + } + }, + 'click .create-collection' : '_clickCreate' + }, + + // ........................................................................ header + /** expand help */ + _clickMoreHelp : function( ev ){ + this.$( '.main-help' ).css( 'max-height', 'none' ); + this.$( '.main-help .help-content p:first-child' ).css( 'white-space', 'normal' ); + this.$( '.more-help' ).hide(); + }, + /** collapse help */ + _clickLessHelp : function( ev ){ + this.$( '.main-help' ).css( 'max-height', '' ); + this.$( '.main-help .help-content p:first-child' ).css( 'white-space', '' ); + this.$( '.more-help' ).show(); + }, + + /** show an alert on the top of the interface containing message (alertClass is bootstrap's alert-*)*/ + _showAlert : function( message, alertClass ){ + alertClass = alertClass || 'alert-danger'; + this.$( '.main-help' ).hide(); + this.$( '.header .alert' ).attr( 'class', 'alert alert-dismissable' ).addClass( alertClass ).show() + .find( '.alert-message' ).html( message ); + }, + /** hide the alerts at the top */ + _hideAlert : function( message ){ + this.$( '.main-help' ).show(); + this.$( '.header .alert' ).hide(); + }, + + //TODO: consolidate these + /** toggle between showing only unpaired and split view */ + _clickShowOnlyUnpaired : function( ev ){ + //console.debug( 'click unpaired', ev.currentTarget ); + if( this.$( '.paired-columns' ).is( ':visible' ) ){ + this.hidePaired(); + } else { + this.splitView(); + } + }, + /** toggle between showing only paired and split view */ + _clickShowOnlyPaired : function( ev ){ + //console.debug( 'click paired' ); + if( this.$( '.unpaired-columns' ).is( ':visible' ) ){ + this.hideUnpaired(); + } else { + this.splitView(); + } + }, + /** hide unpaired, show paired */ + hideUnpaired : function( speed, callback ){ + speed = speed || 0; + this.$( '.unpaired-columns' ).hide( speed, callback ); + //this.$( '.unpaired-filter' ).hide( speed ); + this.$( '.paired-columns' ).show( speed ).css( 'flex', '1 0 auto' ); + this.unpairedPanelHidden = true; + }, + /** hide paired, show unpaired */ + hidePaired : function( speed, callback ){ + speed = speed || 0; + this.$( '.unpaired-columns' ).show( speed ).css( 'flex', '1 0 auto' ); + //this.$( '.unpaired-filter' ).show( speed ); + this.$( '.paired-columns' ).hide( speed, callback ); + this.pairedPanelHidden = true; + }, + /** show both paired and unpaired (splitting evenly) */ + splitView : function( speed, callback ){ + speed = speed || 0; + this.unpairedPanelHidden = this.pairedPanelHidden = false; + //this.$( '.unpaired-filter' ).show( speed ); + this._renderMiddle( speed ); + return this; + }, + + /** unpair all paired and do other super neat stuff which I'm not really sure about yet... */ + _clickUnpairAll : function( ev ){ + this.unpairAll(); + }, + + /** attempt to autopair */ + _clickAutopair : function( ev ){ + var paired = this.autoPair(); + //console.debug( 'autopaired', paired ); + //TODO: an indication of how many pairs were found - if 0, assist + this.trigger( 'autopair', paired ); + }, + + /** set the filters based on the data attributes of the button click target */ + _clickFilterChoice : function( ev ){ + var $selected = $( ev.currentTarget ); + this.$( '.forward-unpaired-filter input' ).val( $selected.data( 'forward' ) ); + this.$( '.reverse-unpaired-filter input' ).val( $selected.data( 'reverse' ) ); + this._hideChooseFilters(); + this.trigger( 'filter-change' ); + }, + + /** hide the choose filters popover */ + _hideChooseFilters : function(){ + //TODO: update bootstrap and remove the following hack + // see also: https://github.com/twbs/bootstrap/issues/10260 + this.$( '.choose-filters-link' ).popover( 'hide' ); + this.$( '.popover' ).css( 'display', 'none' ); + }, + + /** clear both filters */ + _clearFilters : function( ev ){ + this.$( '.forward-unpaired-filter input' ).val( '' ); + this.$( '.reverse-unpaired-filter input' ).val( '' ); + this.trigger( 'filter-change' ); + }, + + // ........................................................................ unpaired + /** select an unpaired dataset */ + _clickUnpairedDataset : function( ev ){ + ev.stopPropagation(); + return this.toggleSelectUnpaired( $( ev.currentTarget ) ); + }, + + /** Toggle the selection of an unpaired dataset representation. + * @param [jQuery] $dataset the unpaired dataset dom rep to select + * @param [Boolean] options.force if defined, force selection based on T/F; otherwise, toggle + */ + toggleSelectUnpaired : function( $dataset, options ){ + options = options || {}; + var dataset = $dataset.data( 'dataset' ), + select = options.force !== undefined? options.force: !$dataset.hasClass( 'selected' ); + //console.debug( id, options.force, $dataset, dataset ); + if( !$dataset.size() || dataset === undefined ){ return $dataset; } + + if( select ){ + $dataset.addClass( 'selected' ); + if( !options.waitToPair ){ + this.pairAllSelected(); + } + + } else { + $dataset.removeClass( 'selected' ); + //delete dataset.selected; + } + return $dataset; + }, + + /** pair all the currently selected unpaired datasets */ + pairAllSelected : function( options ){ + options = options || {}; + var creator = this, + fwds = [], + revs = [], + pairs = []; + //TODO: could be made more concise + creator.$( '.unpaired-columns .forward-column .dataset.selected' ).each( function(){ + fwds.push( $( this ).data( 'dataset' ) ); + }); + creator.$( '.unpaired-columns .reverse-column .dataset.selected' ).each( function(){ + revs.push( $( this ).data( 'dataset' ) ); + }); + fwds.length = revs.length = Math.min( fwds.length, revs.length ); + //console.debug( fwds ); + //console.debug( revs ); + fwds.forEach( function( fwd, i ){ + try { + pairs.push( creator._pair( fwd, revs[i], { silent: true }) ); + + } catch( err ){ + //TODO: preserve selected state of those that couldn't be paired + //TODO: warn that some could not be paired + console.error( err ); + } + }); + if( pairs.length && !options.silent ){ + this.trigger( 'pair:new', pairs ); + } + return pairs; + }, + + /** clear the selection on all unpaired datasets */ + clearSelectedUnpaired : function(){ + this.$( '.unpaired-columns .dataset.selected' ).removeClass( 'selected' ); + }, + + /** attempt to pair two datasets directly across from one another */ + _clickPairRow : function( ev ){ + //if( !ev.currentTarget ){ return true; } + var rowIndex = $( ev.currentTarget ).index(), + fwd = $( '.unpaired-columns .forward-column .dataset' ).eq( rowIndex ).data( 'dataset' ), + rev = $( '.unpaired-columns .reverse-column .dataset' ).eq( rowIndex ).data( 'dataset' ); + //console.debug( 'row:', rowIndex, fwd, rev ); + //TODO: animate + this._pair( fwd, rev ); + }, + + // ........................................................................ divider/partition + /** start dragging the visible divider/partition between unpaired and paired panes */ + _startPartitionDrag : function( ev ){ + var creator = this, + startingY = ev.pageY; + //console.debug( 'partition drag START:', ev ); + $( 'body' ).css( 'cursor', 'ns-resize' ); + creator.$( '.flexible-partition-drag' ).css( 'color', 'black' ); + + function endDrag( ev ){ + //console.debug( 'partition drag STOP:', ev ); + // doing this by an added class didn't really work well - kept flashing still + creator.$( '.flexible-partition-drag' ).css( 'color', '' ); + $( 'body' ).css( 'cursor', '' ).unbind( 'mousemove', trackMouse ); + } + function trackMouse( ev ){ + var offset = ev.pageY - startingY; + if( !creator.adjPartition( offset ) ){ + $( 'body' ).trigger( 'mouseup' ); + } + startingY += offset; + } + $( 'body' ).mousemove( trackMouse ); + $( 'body' ).one( 'mouseup', endDrag ); + }, + + /** adjust the parition up/down +/-adj pixels */ + adjPartition : function( adj ){ + var $unpaired = this.$( '.unpaired-columns' ), + $paired = this.$( '.paired-columns' ), + unpairedHi = parseInt( $unpaired.css( 'height' ), 10 ), + pairedHi = parseInt( $paired.css( 'height' ), 10 ); + //console.debug( adj, 'hi\'s:', unpairedHi, pairedHi, unpairedHi + adj, pairedHi - adj ); + + unpairedHi = Math.max( 10, unpairedHi + adj ); + pairedHi = pairedHi - adj; + + if( unpairedHi <= 10 ){ + this.hideUnpaired(); + return false; + } else if( !$unpaired.is( 'visible' ) ){ + $unpaired.show(); + //this.$( '.unpaired-filter' ).show(); + } + + if( pairedHi <= 15 ){ + this.hidePaired(); + if( pairedHi < 10 ){ return false; } + + } else if( !$paired.is( 'visible' ) ){ + $paired.show(); + } + + $unpaired.css({ + height : unpairedHi + 'px', + flex : '0 0 auto' + }); + return true; + }, + + // ........................................................................ paired + /** rename a pair when the pair name is clicked */ + _clickPairName : function( ev ){ + var $control = $( ev.currentTarget ), + pair = this.paired[ $control.parent().index() ], + response = prompt( 'Enter a new name for the pair:', pair.name ); + if( response ){ + pair.name = response; + $control.text( pair.name ); + } + }, + + /** unpair this pair */ + _clickUnpair : function( ev ){ + //if( !ev.currentTarget ){ return true; } + //TODO: this is a hack bc each paired rev now has two elems (dataset, button) + var pairIndex = Math.floor( $( ev.currentTarget ).index() / 2 ); + //console.debug( 'pair:', pairIndex ); + //TODO: animate + this._unpair( this.paired[ pairIndex ] ); + }, + + //TODO: the following is ridiculous + _hoverPaired : function( ev ){ + var $target = $( ev.currentTarget ), + index = $target.index(); + //TODO: this is a hack bc each paired rev now has two elems (dataset, button) + if( $target.parents( '.reverse-column' ).size() ){ + index = Math.floor( index / 2 ); + } + //console.debug( 'index:', index ); + this.emphasizePair( index ); + }, + _hoverOutPaired : function( ev ){ + var $target = $( ev.currentTarget ), + index = $target.index(); + //TODO: this is a hack bc each paired rev now has two elems (dataset, button) + if( $target.parents( '.reverse-column' ).size() ){ + index = Math.floor( index / 2 ); + } + //console.debug( 'index:', index ); + this.deemphasizePair( index ); + }, + emphasizePair : function( index ){ + //console.debug( 'emphasizePairedBorder:', index ); + this.$( '.paired-columns .forward-column .dataset.paired' ).eq( index ) + .add( this.$( '.paired-columns .paired-column .dataset.paired' ).eq( index ) ) + .add( this.$( '.paired-columns .reverse-column .dataset.paired' ).eq( index ) ) + .addClass( 'emphasized' ); + }, + deemphasizePair : function( index ){ + //console.debug( 'deemphasizePairedBorder:', index ); + this.$( '.paired-columns .forward-column .dataset.paired' ).eq( index ) + .add( this.$( '.paired-columns .paired-column .dataset.paired' ).eq( index ) ) + .add( this.$( '.paired-columns .reverse-column .dataset.paired' ).eq( index ) ) + .removeClass( 'emphasized' ); + }, + + // ........................................................................ footer + /** handle a collection name change */ + _changeName : function( ev ){ + this._validationWarning( 'name', !!this._getName() ); + }, + + /** get the current collection name */ + _getName : function(){ + return _.escape( this.$( '.collection-name' ).val() ); + }, + + /** attempt to create the current collection */ + _clickCreate : function( ev ){ + var name = this._getName(); + if( !name ){ + this._validationWarning( 'name' ); + } else { + this.createList(); + } + }, + + // ------------------------------------------------------------------------ misc + /** debug a dataset list */ + _printList : function( list ){ + var creator = this; + _.each( list, function( e ){ + if( list === creator.paired ){ + creator._printPair( e ); + } else { + //console.debug( e ); + } + }); + }, + + /** print a pair Object */ + _printPair : function( pair ){ + console.debug( pair.forward.name, pair.reverse.name, ': ->', pair.name ); + }, + + /** string rep */ + toString : function(){ return 'PairedCollectionCreator'; } +}); + + +//TODO: move to require text plugin and load these as text +//TODO: underscore currently unnecc. bc no vars are used +//TODO: better way of localizing text-nodes in long strings +/** underscore template fns attached to class */ +PairedCollectionCreator.templates = PairedCollectionCreator.templates || { +/** the skeleton */ +main : _.template([ + '<div class="header"></div>', + '<div class="middle"></div>', + '<div class="footer">' +].join('')), + +/** the header (not including help text) */ +header : _.template([ + '<div class="main-help well clear">', + '<a class="more-help" href="javascript:void(0);">', _l( 'More help' ), '</a>', + '<div class="help-content">', + '<a class="less-help" href="javascript:void(0);">', _l( 'Less' ), '</a>', + '</div>', + '</div>', + '<div class="alert alert-dismissable">', + '<button type="button" class="close" data-dismiss="alert" aria-hidden="true">×</button>', + '<span class="alert-message"></span>', + '</div>', + + '<div class="column-headers vertically-spaced row-flex-container">', + '<div class="forward-column flex-column column">', + '<div class="column-header">', + '<div class="column-title">', + '<span class="title">', _l( 'Unpaired forward' ), '</span>', + '<span class="title-info unpaired-info"></span>', + '</div>', + '<div class="unpaired-filter forward-unpaired-filter pull-left">', + '<input class="search-query" placeholder="', _l( 'Filter this list' ), '" />', + '</div>', + '</div>', + '</div>', + '<div class="paired-column flex-column column">', + '<div class="column-header">', + '<a class="choose-filters-link" href="javascript:void(0)">', + _l( 'Choose filters' ), + '</a>', + '<a class="clear-filters-link" href="javascript:void(0);">', + _l( 'Clear filters' ), + '</a><br />', + '<a class="autopair-link" href="javascript:void(0);">', + _l( 'Auto-pair' ), + '</a>', + '</div>', + '</div>', + '<div class="reverse-column flex-column column">', + '<div class="column-header">', + '<div class="column-title">', + '<span class="title">', _l( 'Unpaired reverse' ), '</span>', + '<span class="title-info unpaired-info"></span>', + '</div>', + '<div class="unpaired-filter reverse-unpaired-filter pull-left">', + '<input class="search-query" placeholder="', _l( 'Filter this list' ), '" />', + '</div>', + '</div>', + '</div>', + '</div>' +].join('')), + +/** the middle: unpaired, divider, and paired */ +middle : _.template([ + '<div class="unpaired-columns row-flex-container scroll-container">', + '<div class="forward-column flex-column column">', + '<ol class="column-datasets"></ol>', + '</div>', + '<div class="paired-column flex-column column">', + '<ol class="column-datasets"></ol>', + '</div>', + '<div class="reverse-column flex-column column">', + '<ol class="column-datasets"></ol>', + '</div>', + '</div>', + '<div class="flexible-partition">', + '<div class="flexible-partition-drag"></div>', + '<div class="column-header">', + '<div class="column-title paired-column-title">', + '<span class="title"></span>', + '</div>', + '<a class="unpair-all-link" href="javascript:void(0);">', + _l( 'Unpair all' ), + '</a>', + '</div>', + '</div>', + '<div class="paired-columns row-flex-container scroll-container">', + '<div class="forward-column flex-column column">', + '<ol class="column-datasets"></ol>', + '</div>', + '<div class="paired-column flex-column column">', + '<ol class="column-datasets"></ol>', + '</div>', + '<div class="reverse-column flex-column column">', + '<ol class="column-datasets"></ol>', + '</div>', + '</div>' +].join('')), + +/** creation and cancel controls */ +footer : _.template([ + '<div class="attributes clear">', + '<input class="collection-name form-control pull-right" ', + 'placeholder="', _l( 'Enter a name for your new list' ), '" />', + '<div class="collection-name-prompt pull-right">', _l( 'Name' ), ':</div>', + '</div>', + + '<div class="actions clear vertically-spaced">', + '<div class="other-options pull-left">', + '<button class="cancel-create btn" tabindex="-1">', _l( 'Cancel' ), '</button>', + '<div class="create-other btn-group dropup">', + '<button class="btn btn-default dropdown-toggle" data-toggle="dropdown">', + _l( 'Create a different kind of collection' ), + ' <span class="caret"></span>', + '</button>', + '<ul class="dropdown-menu" role="menu">', + '<li><a href="#">', _l( 'Create a <i>single</i> pair' ), '</a></li>', + '<li><a href="#">', _l( 'Create a list of <i>unpaired</i> datasets' ), '</a></li>', + '</ul>', + '</div>', + '</div>', + + '<div class="main-options pull-right">', + '<button class="create-collection btn btn-primary">', _l( 'Create list' ), '</button>', + '</div>', + '</div>' +].join('')), + +/** help content */ +helpContent : _.template([ + '<p>', _l([ + 'Collections of paired datasets are ordered lists of dataset pairs (often forward and reverse ', + 'reads) that can be passed to tools and workflows in order to have analyses done on the entire ', + 'group. This interface allows you to create a collection, choose which datasets are paired, ', + 'and re-order the final collection.' + ].join( '' )), '</p>', + '<p>', _l([ + 'Unpaired datasets are shown in the <i data-target=".unpaired-columns">unpaired section</i> ', + '(hover over the underlined words to highlight below). ', + 'Paired datasets are shown in the <i data-target=".paired-columns">paired section</i>.', + '<ul>To pair datasets, you can:', + '<li>Click a dataset in the ', + '<i data-target=".unpaired-columns .forward-column .column-datasets,', + '.unpaired-columns .forward-column">forward column</i> ', + 'to select it then click a dataset in the ', + '<i data-target=".unpaired-columns .reverse-column .column-datasets,', + '.unpaired-columns .reverse-column">reverse column</i>.', + '</li>', + '<li>Click one of the "Pair these datasets" buttons in the ', + '<i data-target=".unpaired-columns .paired-column .column-datasets,', + '.unpaired-columns .paired-column">middle column</i> ', + 'to pair the datasets in a particular row.', + '</li>', + '<li>Click <i data-target=".autopair-link">"Auto-pair"</i> ', + 'to have your datasets automatically paired based on name.', + '</li>', + '</ul>' + ].join( '' )), '</p>', + '<p>', _l([ + '<ul>You can filter what is shown in the unpaired sections by:', + '<li>Entering partial dataset names in either the ', + '<i data-target=".forward-unpaired-filter input">forward filter</i> or ', + '<i data-target=".reverse-unpaired-filter input">reverse filter</i>.', + '</li>', + '<li>Choosing from a list of preset filters by clicking the ', + '<i data-target=".choose-filters-link">"Choose filters" link</i>.', + '</li>', + '<li>Clearing the filters by clicking the ', + '<i data-target=".clear-filters-link">"Clear filters" link</i>.', + '</li>', + '</ul>' + ].join( '' )), '</p>', + '<p>', _l([ + 'To unpair individual dataset pairs, click the ', + '<i data-target=".unpair-btn">unpair buttons ( <span class="fa fa-unlink"></span> )</i>. ', + 'Click the <i data-target=".unpair-all-link">"Unpair all" link</i> to unpair all pairs.' + ].join( '' )), '</p>', + '<p>', _l([ + '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('')) +} + +//============================================================================= +//TODO: to own file +/* +(Imported for edit distance algorith. From: https://gist.github.com/andrei-m/982927) +Copyright (c) 2011 Andrei Mackenzie +*/ +// Compute the edit distance between the two given strings +//exports.getEditDistance = function(a, b){ +function levenshteinDistance(a, b){ + if(a.length === 0){ return b.length; } + if(b.length === 0){ return a.length; } + + var matrix = []; + + // increment along the first column of each row + var i; + for(i = 0; i <= b.length; i++){ + matrix[i] = [i]; + } + + // increment each column in the first row + var j; + for(j = 0; j <= a.length; j++){ + matrix[0][j] = j; + } + + // Fill in the rest of the matrix + for(i = 1; i <= b.length; i++){ + for(j = 1; j <= a.length; j++){ + if(b.charAt(i-1) === a.charAt(j-1)){ + matrix[i][j] = matrix[i-1][j-1]; + } else { + matrix[i][j] = Math.min(matrix[i-1][j-1] + 1, // substitution + Math.min(matrix[i][j-1] + 1, // insertion + matrix[i-1][j] + 1)); // deletion + } + } + } + + //console.debug( '\t\t levenshteinDistance', a, b, matrix[b.length][a.length] ); + return matrix[b.length][a.length]; +} + + +//============================================================================= +(function(){ + /** plugin that will highlight an element when this element is hovered over */ + jQuery.fn.extend({ + hoverhighlight : function $hoverhighlight( scope, color ){ + scope = scope || 'body'; + if( !this.size() ){ return this; } + + $( this ).each( function(){ + var $this = $( this ), + targetSelector = $this.data( 'target' ); + + if( targetSelector ){ + $this.mouseover( function( ev ){ + $( targetSelector, scope ).css({ + background: color + }); + }) + .mouseout( function( ev ){ + $( targetSelector ).css({ + background: '' + }); + }); + } + }); + return this; + } + }); +}()); + + +//============================================================================= +//TODO: to own file +/** a modal version of the paired collection creator */ +var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){ + options = _.defaults( options || {}, { + datasets : datasets, + oncancel : function(){ Galaxy.modal.hide(); }, + oncreate : function(){ + Galaxy.modal.hide(); + Galaxy.currHistoryPanel.refreshContents(); + } + }); + + if( !window.Galaxy || !Galaxy.modal ){ + throw new Error( 'Galaxy or Galaxy.modal not found' ); + } + + var creator = new PairedCollectionCreator( options ).render(); + Galaxy.modal.show({ + title : 'Create a collection of paired datasets', + body : creator.$el, + width : '80%', + height : '700px', + closing_events: true + }); + //TODO: remove modal header + return creator; +}; + + +//============================================================================= + return { + PairedCollectionCreator : PairedCollectionCreator, + pairedCollectionCreatorModal : pairedCollectionCreatorModal + }; +}); diff -r e8c791f71470aed7da9c3418f2f7cc754dff1fd6 -r 4d11f590b0a4389f6d9e5b30573acdcbc07e4fe6 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -239,16 +239,43 @@ html: _l( 'Build Dataset List (Experimental)' ), func: function() { panel.getSelectedHdaCollection().promoteToHistoryDatasetCollection( panel.model, "list" ); } - } ); + }); actions.push( { // TODO: Only show quick pair if two things selected. html: _l( 'Build Dataset Pair (Experimental)' ), func: function() { panel.getSelectedHdaCollection().promoteToHistoryDatasetCollection( panel.model, "paired" ); } - } ); + }); + actions.push( { + // TODO: Only show quick pair if two things selected. + html: _l( 'Build List of Dataset Pairs (Experimental)' ), + func: panel._showPairedCollectionModal.bind( panel ) + }); return new PopupMenu( $where.find( '.history-dataset-action-popup-btn' ), actions ); }, + _showPairedCollectionModal : function(){ + var panel = this, + datasets = panel.getSelectedHdaCollection().toJSON().filter( function( content ){ + return content.history_content_type === 'dataset' + && content.state === hdaModel.HistoryDatasetAssociation.STATES.OK; + }); + if( datasets.length ){ + require([ 'mvc/collection/paired-collection-creator' ], function( creator ){ + window.creator = creator.pairedCollectionCreatorModal( datasets, { + historyId : panel.model.id + }); + }); + } else { + //Galaxy.modal.show({ + // body : _l( 'No valid datasets were selected' ), + // buttons : { + // 'Ok': function(){ Galaxy.modal.hide(); } + // } + //}); + } + }, + // ------------------------------------------------------------------------ hda sub-views /** If this hda is deleted and we're not showing deleted hdas, remove the view * @param {HistoryDataAssociation} the hda to check diff -r e8c791f71470aed7da9c3418f2f7cc754dff1fd6 -r 4d11f590b0a4389f6d9e5b30573acdcbc07e4fe6 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,b,h,d,a,c,e){var g=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(i){i=i||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=i.purgeAllowed||false;this.selecting=i.selecting||false;this.annotationEditorShown=i.annotationEditorShown||false;this.tagsEditorShown=i.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,i)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(i){this.model.fetch()},this)},renderModel:function(){var i=$("<div/>");i.append(g.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(i);this._renderAnnotation(i)}i.find(".history-secondary-actions").prepend(this._renderSelectButton());i.find(".history-dataset-actions").toggle(this.selecting);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDATagEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDATagEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".history-secondary-actions"))})},_renderAnnotation:function(i){var j=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:i.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDAAnnotationEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDAAnnotationEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".history-secondary-actions"))})},_renderSelectButton:function(i){return faIconButton({title:e("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(i){i=i||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,i);if(!this.model){return}this._setUpDatasetActionsPopup(i);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var j=this;i.find(".history-name").attr("title",e("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(k){var l=j.model.get("name");if(k&&k!==l){j.$el.find(".history-name").text(k);j.model.save({name:k}).fail(function(){j.$el.find(".history-name").text(j.model.previous("name"))})}else{j.$el.find(".history-name").text(l)}}})},_setUpDatasetActionsPopup:function(i){var j=this,k=[{html:e("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;j.getSelectedHdaCollection().ajaxQueue(l)}}];if(j.purgeAllowed){k.push({html:e("Permanently delete datasets"),func:function(){if(confirm(e("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;j.getSelectedHdaCollection().ajaxQueue(l)}}})}k.push({html:e("Build Dataset List (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"list")}});k.push({html:e("Build Dataset Pair (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"paired")}});return new PopupMenu(i.find(".history-dataset-action-popup-btn"),k)},_handleHdaDeletionChange:function(i){if(i.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[i.id])}},_handleHdaVisibleChange:function(i){if(i.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[i.id])}},_createContentView:function(j){var i=j.id,l=j.get("history_content_type"),k=null;if(l==="dataset"){k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(l==="dataset_collection"){k=new h.DatasetCollectionEditView({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,j);j.on("selected",function(m,l){if(!l){return}var k=[];if((l.shiftKey)&&(i.lastSelectedViewId&&_.has(i.hdaViews,i.lastSelectedViewId))){var o=i.hdaViews[i.lastSelectedViewId];k=i.selectDatasetRange(m,o).map(function(p){return p.model.id})}else{var n=m.model.id;i.lastSelectedViewId=n;k=[n]}i.selectedHdaIds=_.union(i.selectedHdaIds,k)});j.on("de-selected",function(l,k){var m=l.model.id;i.selectedHdaIds=_.without(i.selectedHdaIds,m)})},toggleHDATagEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.annotationEditor){k.annotationEditor.toggle.apply(k.annotationEditor,j)}})},removeHdaView:function(j){if(!j){return}var i=this;j.$el.fadeOut(i.fxSpeed,function(){j.off();j.remove();delete i.hdaViews[j.model.id];if(_.isEmpty(i.hdaViews)){i.trigger("empty-history",i);i._renderEmptyMsg()}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(i);_.each(this.hdaViews,function(j){j.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(i);_.each(this.hdaViews,function(j){j.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.select(i)})},deselectAllDatasets:function(i){this.lastSelectedViewId=null;_.each(this.hdaViews,function(j){j.deselect(i)})},selectDatasetRange:function(k,j){var i=this.hdaViewRange(k,j);_.each(i,function(l){l.select()});return i},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(i){return i.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(i){return i.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:g}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/collection/dataset-collection-edit","mvc/history/readonly-history-panel","mvc/tags","mvc/annotations","utils/localization"],function(f,b,h,d,a,c,e){var g=d.ReadOnlyHistoryPanel.extend({HDAViewClass:b.HDAEditView,initialize:function(i){i=i||{};this.selectedHdaIds=[];this.lastSelectedViewId=null;this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=i.purgeAllowed||false;this.selecting=i.selecting||false;this.annotationEditorShown=i.annotationEditorShown||false;this.tagsEditorShown=i.tagsEditorShown||false;d.ReadOnlyHistoryPanel.prototype.initialize.call(this,i)},_setUpModelEventHandlers:function(){d.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this._handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this._handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(i){this.model.fetch()},this)},renderModel:function(){var i=$("<div/>");i.append(g.templates.historyPanel(this.model.toJSON()));this.$emptyMessage(i).text(this.emptyMsg);if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(i);this._renderAnnotation(i)}i.find(".history-secondary-actions").prepend(this._renderSelectButton());i.find(".history-dataset-actions").toggle(this.selecting);i.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(i);this.renderHdas(i);return i},_renderTags:function(i){var j=this;this.tagsEditor=new a.TagsEditor({model:this.model,el:i.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDATagEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDATagEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(i.find(".history-secondary-actions"))})},_renderAnnotation:function(i){var j=this;this.annotationEditor=new c.AnnotationEditor({model:this.model,el:i.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){j.toggleHDAAnnotationEditors(true,j.fxSpeed)},onhide:function(){j.toggleHDAAnnotationEditors(false,j.fxSpeed)},$activator:faIconButton({title:e("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(i.find(".history-secondary-actions"))})},_renderSelectButton:function(i){return faIconButton({title:e("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(i){i=i||this.$el;d.ReadOnlyHistoryPanel.prototype._setUpBehaviours.call(this,i);if(!this.model){return}this._setUpDatasetActionsPopup(i);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var j=this;i.find(".history-name").attr("title",e("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(k){var l=j.model.get("name");if(k&&k!==l){j.$el.find(".history-name").text(k);j.model.save({name:k}).fail(function(){j.$el.find(".history-name").text(j.model.previous("name"))})}else{j.$el.find(".history-name").text(l)}}})},_setUpDatasetActionsPopup:function(i){var j=this,k=[{html:e("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];j.getSelectedHdaCollection().ajaxQueue(l)}},{html:e("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;j.getSelectedHdaCollection().ajaxQueue(l)}}];if(j.purgeAllowed){k.push({html:e("Permanently delete datasets"),func:function(){if(confirm(e("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;j.getSelectedHdaCollection().ajaxQueue(l)}}})}k.push({html:e("Build Dataset List (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"list")}});k.push({html:e("Build Dataset Pair (Experimental)"),func:function(){j.getSelectedHdaCollection().promoteToHistoryDatasetCollection(j.model,"paired")}});k.push({html:e("Build List of Dataset Pairs (Experimental)"),func:j._showPairedCollectionModal.bind(j)});return new PopupMenu(i.find(".history-dataset-action-popup-btn"),k)},_showPairedCollectionModal:function(){var i=this,j=i.getSelectedHdaCollection().toJSON().filter(function(k){return k.history_content_type==="dataset"&&k.state===f.HistoryDatasetAssociation.STATES.OK});if(j.length){require(["mvc/collection/paired-collection-creator"],function(k){window.creator=k.pairedCollectionCreatorModal(j,{historyId:i.model.id})})}else{}},_handleHdaDeletionChange:function(i){if(i.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[i.id])}},_handleHdaVisibleChange:function(i){if(i.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[i.id])}},_createContentView:function(j){var i=j.id,l=j.get("history_content_type"),k=null;if(l==="dataset"){k=new this.HDAViewClass({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],selectable:this.selecting,purgeAllowed:this.purgeAllowed,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)})}else{if(l==="dataset_collection"){k=new h.DatasetCollectionEditView({model:j,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[i],hasUser:this.model.ownedByCurrUser(),logger:this.logger})}}this._setUpHdaListeners(k);return k},_setUpHdaListeners:function(j){var i=this;d.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,j);j.on("selected",function(m,l){if(!l){return}var k=[];if((l.shiftKey)&&(i.lastSelectedViewId&&_.has(i.hdaViews,i.lastSelectedViewId))){var o=i.hdaViews[i.lastSelectedViewId];k=i.selectDatasetRange(m,o).map(function(p){return p.model.id})}else{var n=m.model.id;i.lastSelectedViewId=n;k=[n]}i.selectedHdaIds=_.union(i.selectedHdaIds,k)});j.on("de-selected",function(l,k){var m=l.model.id;i.selectedHdaIds=_.without(i.selectedHdaIds,m)})},toggleHDATagEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(i){var j=arguments;_.each(this.hdaViews,function(k){if(k.annotationEditor){k.annotationEditor.toggle.apply(k.annotationEditor,j)}})},removeHdaView:function(j){if(!j){return}var i=this;j.$el.fadeOut(i.fxSpeed,function(){j.off();j.remove();delete i.hdaViews[j.model.id];if(_.isEmpty(i.hdaViews)){i.trigger("empty-history",i);i._renderEmptyMsg()}})},events:_.extend(_.clone(d.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":"toggleSelectors","click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=true;this.$(".history-dataset-actions").slideDown(i);_.each(this.hdaViews,function(j){j.showSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},hideSelectors:function(i){i=(i!==undefined)?(i):(this.fxSpeed);this.selecting=false;this.$(".history-dataset-actions").slideUp(i);_.each(this.hdaViews,function(j){j.hideSelector()});this.selectedHdaIds=[];this.lastSelectedViewId=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAllDatasets:function(i){_.each(this.hdaViews,function(j){j.select(i)})},deselectAllDatasets:function(i){this.lastSelectedViewId=null;_.each(this.hdaViews,function(j){j.deselect(i)})},selectDatasetRange:function(k,j){var i=this.hdaViewRange(k,j);_.each(i,function(l){l.select()});return i},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(i){return i.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(i){return i.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:g}}); \ No newline at end of file diff -r e8c791f71470aed7da9c3418f2f7cc754dff1fd6 -r 4d11f590b0a4389f6d9e5b30573acdcbc07e4fe6 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1360,7 +1360,53 @@ .toast-error{background-color:#bd362f} .toast-info{background-color:#2f96b4} .toast-warning{background-color:#f89406} -@media all and (max-width:240px){#toast-container>div{padding:8px 8px 8px 50px;width:11em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:241px) and (max-width:480px){#toast-container>div{padding:8px 8px 8px 50px;width:18em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:481px) and (max-width:768px){#toast-container>div{padding:15px 15px 15px 50px;width:25em}}.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none} +@media all and (max-width:240px){#toast-container>div{padding:8px 8px 8px 50px;width:11em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:241px) and (max-width:480px){#toast-container>div{padding:8px 8px 8px 50px;width:18em} #toast-container .toast-close-button{right:-0.2em;top:-0.2em}}@media all and (min-width:481px) and (max-width:768px){#toast-container>div{padding:15px 15px 15px 50px;width:25em}}.collection-creator{height:100%;display:flex;flex-direction:column;align-items:stretch;align-content:stretch;overflow:hidden;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none}.collection-creator ol,.collection-creator li{list-style:none;padding:0;margin:0} +.collection-creator>*:not(.popover){padding:0px 8px 0px 8px} +.collection-creator .btn{border-color:#BFBFBF} +.collection-creator .vertically-spaced{margin-top:8px} +.collection-creator .scroll-container{overflow:auto} +.collection-creator .truncate{overflow:hidden;white-space:nowrap;text-overflow:ellipsis} +.collection-creator .empty-message{color:grey;font-style:italic} +.collection-creator .choose-filters .help{margin-bottom:2px;font-size:90%;color:grey} +.collection-creator .choose-filters button{width:100%;margin-top:2px} +.collection-creator .header .alert{display:none} +.collection-creator .column{width:30%} +.collection-creator .column-title{height:22px;line-height:22px;overflow:hidden}.collection-creator .column-title:hover{text-decoration:underline;cursor:pointer} +.collection-creator .column-title .title{font-weight:bold} +.collection-creator .column-title .title-info{color:grey}.collection-creator .column-title .title-info:before{content:' - '} +.collection-creator .paired-column{text-align:center;width:22%;flex:0 1 auto} +.collection-creator .header{flex:0 0 auto;padding-bottom:8px}.collection-creator .header .main-help{max-height:36px;margin-bottom:16px;overflow:hidden;padding:8px;background:#f8f8f8}.collection-creator .header .main-help .help-content i{cursor:help;border-bottom:1px dotted grey;font-style:normal} +.collection-creator .header .main-help .help-content ul,.collection-creator .header .main-help .help-content li{list-style:circle;margin-left:16px} +.collection-creator .header .main-help .help-content p:first-child{overflow:hidden;white-space:nowrap;text-overflow:ellipsis} +.collection-creator .header .main-help .help-content .less-help{display:inline-block;width:100%;text-align:right} +.collection-creator .header .main-help .more-help{float:right} +.collection-creator .header .column-headers .column-header .unpaired-filter{width:100%}.collection-creator .header .column-headers .column-header .unpaired-filter .search-query{width:100%;height:22px} +.collection-creator .header .paired-column a:not(:last-child){margin-right:8px} +.collection-creator .header .reverse-column .column-title{text-align:right} +.collection-creator .row-flex-container{display:flex;flex-direction:row;align-items:stretch;align-content:stretch} +.collection-creator .flex-column{flex:1 1 auto} +.collection-creator .middle{flex:1 0 auto;display:flex;flex-direction:column;align-items:stretch;align-content:stretch} +.collection-creator .unpaired-columns,.collection-creator .paired-columns{flex:1 0 auto;height:0;border:1px solid lightgrey;border-radius:3px;border-width:1px 0 1px 0;overflow-y:auto;padding:4px} +.collection-creator .unpaired-columns{flex:1 0 auto} +.collection-creator .paired-columns{margin-bottom:8px} +.collection-creator .column-datasets{list-style:none;overflow:hidden}.collection-creator .column-datasets .dataset{height:32px;margin-bottom:2px;border:1px solid lightgrey;border-radius:3px;padding:0 8px 0 8px;line-height:28px;cursor:pointer;overflow:hidden}.collection-creator .column-datasets .dataset:last-child{margin-bottom:4px} +.collection-creator .unpaired-columns .dataset.unpaired{border-color:grey}.collection-creator .unpaired-columns .dataset.unpaired:hover{border-color:black} +.collection-creator .unpaired-columns .dataset.unpaired.selected{border-color:black;background:black;color:white} +.collection-creator .unpaired-columns .forward-column .dataset.unpaired{margin-right:32px} +.collection-creator .unpaired-columns .paired-column .dataset.unpaired{border-color:lightgrey;color:lightgrey}.collection-creator .unpaired-columns .paired-column .dataset.unpaired:hover{border-color:black;color:black} +.collection-creator .unpaired-columns .reverse-column .dataset.unpaired{text-align:right;margin-left:32px} +.collection-creator .flexible-partition .flexible-partition-drag{width:100%;height:8px;cursor:ns-resize}.collection-creator .flexible-partition .flexible-partition-drag:hover{background:lightgrey} +.collection-creator .flexible-partition .column-header{width:100%;text-align:center}.collection-creator .flexible-partition .column-header .column-title{display:inline;margin-right:8px} +.collection-creator .paired-columns .dataset.paired{background:#AFF1AF;border-color:grey;border-width:2px}.collection-creator .paired-columns .dataset.paired:hover,.collection-creator .paired-columns .dataset.paired.emphasized{border-color:black} +.collection-creator .paired-columns .forward-column .dataset.paired{margin-left:32px;border-radius:3px 0 0 3px;border-right-color:grey;border-right-width:1px;text-align:right}.collection-creator .paired-columns .forward-column .dataset.paired:after{margin-left:8px;font-family:FontAwesome;content:'\f061'} +.collection-creator .paired-columns .paired-column .dataset.paired{border-radius:0;border-width:2px 0 2px 0}.collection-creator .paired-columns .paired-column .dataset.paired .dataset-name:hover{text-decoration:underline} +.collection-creator .paired-columns .reverse-column .dataset.paired{margin-right:32px;border-radius:0 3px 3px 0;border-left-color:grey;border-left-width:1px}.collection-creator .paired-columns .reverse-column .dataset.paired:before{margin-right:8px;font-family:FontAwesome;content:'\f060'} +.collection-creator .paired-columns .reverse-column .unpair-btn{float:right;margin-top:-34px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator .paired-columns .reverse-column .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE} +.collection-creator .footer{flex:0 0 auto;padding-bottom:8px}.collection-creator .footer .collection-name-prompt.validation-warning:before{content:'(required)';margin-right:4px;color:red} +.collection-creator .footer .collection-name{width:50%}.collection-creator .footer .collection-name.validation-warning{border-color:red} +.collection-creator .footer .other-options>*{display:none;margin-left:4px} +.collection-creator .footer .collection-name-prompt{margin:5px 4px 0 0} +.unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none} .parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%} .clear:before,.clear:after{content:" ";display:table;} .clear:after{clear:both} diff -r e8c791f71470aed7da9c3418f2f7cc754dff1fd6 -r 4d11f590b0a4389f6d9e5b30573acdcbc07e4fe6 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -27,6 +27,10 @@ @import "library.less"; @import "toastr.less"; +// UI directory +@import "ui/paired-collection-creator.less"; + + // Mixins .unselectable { diff -r e8c791f71470aed7da9c3418f2f7cc754dff1fd6 -r 4d11f590b0a4389f6d9e5b30573acdcbc07e4fe6 static/style/src/less/ui/paired-collection-creator.less --- /dev/null +++ b/static/style/src/less/ui/paired-collection-creator.less @@ -0,0 +1,365 @@ +// --- main layout elements +.collection-creator { + + height: 100%; + display: flex; + flex-direction: column; + align-items: stretch; + align-content: stretch; + + overflow: hidden; + + -webkit-user-select: none; + -moz-user-select: none; + -ms-user-select: none; + + // ------------------------------------------------------------------------ general + ol, li { + list-style: none; + padding: 0; + margin: 0; + } + > *:not(.popover) { + padding: 0px 8px 0px 8px; + } + .btn { + border-color: #BFBFBF; + } + + .vertically-spaced { + margin-top: 8px; + } + .scroll-container { + overflow: auto; + //overflow-y: scroll; + } + .truncate { + overflow: hidden; + white-space: nowrap; + text-overflow: ellipsis; + } + .empty-message { + color: grey; + font-style: italic; + } + + // ------------------------------------------------------------------------ sub-components + .choose-filters { + .help { + margin-bottom: 2px; + font-size: 90%; + color: grey; + } + button { + width: 100%; + margin-top: 2px; + } + } + + .header .alert { + display: none; + } + + // ------------------------------------------------------------------------ columns + .column { + width: 30%; + } + .column-title { + height: 22px; + line-height: 22px; + overflow: hidden; + &:hover { + text-decoration: underline; + cursor: pointer; + } + .title { + font-weight: bold; + } + .title-info { + color: grey; + &:before { + content: ' - '; + } + } + } + + .paired-column { + text-align: center; + // mess with these two to make center more/less priority + width: 22%; + flex: 0 1 auto; + } + + // ------------------------------------------------------------------------ header + .header { + flex: 0 0 auto; + padding-bottom: 8px; + + .main-help { + max-height: 36px; + margin-bottom: 16px; + overflow: hidden; + padding: 8px; + background: #f8f8f8; + .help-content { + i { + cursor: help; + border-bottom: 1px dotted grey; + font-style: normal; + //font-weight: bold; + //text-decoration: underline; + //text-decoration-style: dashed; + } + ul, li { + list-style: circle; + margin-left: 16px; + } + p:first-child { + overflow: hidden; + white-space: nowrap; + text-overflow: ellipsis; + } + .less-help { + display: inline-block; + width: 100%; + text-align: right; + } + } + .more-help { + //display: inline-block; + float: right; + } + } + .column-headers { + .column-header { + //min-height: 45px; + .unpaired-filter { + width: 100%; + .search-query { + width: 100%; + height: 22px; + } + } + } + } + .paired-column a:not(:last-child) { + margin-right: 8px; + } + .reverse-column .column-title { + text-align: right; + } + + } + + // ------------------------------------------------------------------------ flex + .row-flex-container { + display: flex; + flex-direction: row; + align-items: stretch; + align-content: stretch; + } + .flex-column { + flex: 1 1 auto; + } + + // ------------------------------------------------------------------------ middle + .middle { + // highest flex count - will priority fill with this + flex: 1 0 auto; + + display: flex; + flex-direction: column; + align-items: stretch; + align-content: stretch; + } + .unpaired-columns, + .paired-columns { + flex: 1 0 auto; + // huh! - giving these any static height will pull them in + height: 0; + // NOT setting the above will give a full-height page + + border: 1px solid lightgrey; + border-radius: 3px; + border-width: 1px 0 1px 0; + overflow-y: auto; + padding: 4px; + } + // ------------------------------------------------------------------------ unpaired + .unpaired-columns { + flex: 1 0 auto; + } + + .paired-columns { + margin-bottom: 8px; + } + + // ------------------------------------------------------------------------ middle + // ---- all + .column-datasets { + list-style: none; + overflow: hidden; + + .dataset { + height: 32px; + margin-bottom: 2px; + border: 1px solid lightgrey; + border-radius: 3px; + padding: 0 8px 0 8px; + line-height: 28px; + cursor: pointer; + overflow: hidden; + &:last-child { + margin-bottom: 4px; + } + } + } + + // ---- unpaired + .unpaired-columns { + .dataset.unpaired { + border-color: grey; + &:hover { + border-color: black; + } + &.selected { + border-color: black; + background: black; + color: white; + } + } + .forward-column { + .dataset.unpaired { + margin-right: 32px; + } + } + .paired-column { + .dataset.unpaired { + border-color: lightgrey; + color: lightgrey; + &:hover { + border-color: black; + color: black; + } + } + } + .reverse-column { + .dataset.unpaired { + text-align: right; + margin-left: 32px; + } + } + } + + // ---- paritition/divider + .flexible-partition { + .flexible-partition-drag { + width: 100%; + height: 8px; + cursor: ns-resize; + &:hover { + background: lightgrey; + } + } + .column-header { + width: 100%; + text-align: center; + .column-title { + display: inline; + margin-right: 8px; + } + } + } + + // ---- paired datasets + .paired-columns { + .dataset.paired { + background: #AFF1AF; + border-color: grey; + border-width: 2px; + &:hover, + &.emphasized { + border-color: black; + } + } + .forward-column { + .dataset.paired { + margin-left: 32px; + border-radius: 3px 0 0 3px; + border-right-color: grey; + border-right-width: 1px; + text-align: right; + &:after { + margin-left: 8px; + font-family: FontAwesome; + content: '\f061'; + } + } + } + .paired-column { + .dataset.paired { + border-radius: 0; + border-width: 2px 0 2px 0; + .dataset-name:hover { + text-decoration: underline; + } + } + } + .reverse-column { + .dataset.paired { + margin-right: 32px; + border-radius: 0 3px 3px 0; + border-left-color: grey; + border-left-width: 1px; + &:before { + margin-right: 8px; + font-family: FontAwesome; + content: '\f060'; + } + } + .unpair-btn { + float: right; + margin-top: -34px; + width: 31px; + height: 32px; + //z-index: 1; + border-color: transparent; + //border-color: #BFBFBF; + background: transparent; + font-size: 120%; + &:hover { + border-color: #BFBFBF; + background: #DEDEDE; + } + } + } + } + + // ------------------------------------------------------------------------ footer + .footer { + flex: 0 0 auto; + padding-bottom: 8px; + + .collection-name-prompt.validation-warning:before { + //TODO: localize (somehow) + content: '(required)'; + margin-right: 4px; + color: red; + } + .collection-name { + width: 50%; + &.validation-warning { + border-color: red; + } + } + .other-options > * { + // do not display the links to create other collections yet + display: none; + margin-left: 4px; + } + // actually appears/floats to the left of the input + .collection-name-prompt { + margin: 5px 4px 0 0; + } + } +} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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