commit/galaxy-central: carlfeberhard: UI, Paired collection creator: fixes and refactoring, allow pairs to be selected

Wednesday, 27 August 2014

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/a66a80701913/
Changeset:   a66a80701913
User:        carlfeberhard
Date:        2014-08-27 20:47:54
Summary:     UI, Paired collection creator: fixes and refactoring, allow pairs to be
selected
Affected #:  4 files

diff -r 5a7a7003fbc3bc8f9d56f18a8d4b8f2d5b28fe42 -r
a66a80701913bb99e8abd12235c1ca82dc508f57
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
@@ -5,10 +5,18 @@
 ], function( levelshteinDistance, baseMVC, _l ){
 /* ============================================================================
 TODO:
+    _adjPairedOnScrollBar
+    parition drag now doesn't stop when dragging down
+        can push footer out of modal
+        only *after* partition is all the way down once?
 
 
 PROGRAMMATICALLY:
-h = Galaxy.currHistoryPanel; h.showSelectors(); h.selectAllDatasets(); _.last(
h.actionsPopup.options ).func()
+currPanel.once( 'rendered', function(){
+    currPanel.showSelectors();
+    currPanel.selectAllDatasets();
+    _.last( currPanel.actionsPopup.options ).func();
+});
 
 ============================================================================ */
 /** A view for paired datasets in the collections creator.
@@ -26,7 +34,9 @@
         this.$el.attr( 'draggable', true )
             .html( _.template([
                 '<span class="forward-dataset-name
flex-column"><%= pair.forward.name %></span>',
-                '<span class="pair-name flex-column"><%= pair.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(''), { pair: this.pair }))
             .addClass( 'flex-column-container' );
@@ -661,8 +671,6 @@
             return;
         }
 
-        //this.$( '.unpaired-columns .forward-column' ).lassoable({});
-
         // create the dataset dom arrays
         $rev = split[1].map( function( dataset, i ){
             // if there'll be a fwd dataset across the way, add a button to pair the
row
@@ -685,6 +693,7 @@
         this.$( '.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( $rev ) );
+        this._adjUnpairedOnScrollbar();
     },
     /** return a string to display the count of filtered out datasets */
     _renderUnpairedDisplayStr : function( numFiltered ){
@@ -724,6 +733,18 @@
         this.$( '.unpaired-columns .paired-column .column-datasets'
).empty().prepend( $msg );
         return $msg;
     },
+    /** try to detect if the unpaired section has a scrollbar and adjust left column for
better centering of all */
+    _adjUnpairedOnScrollbar : function(){
+        var $unpairedColumns = this.$( '.unpaired-columns' ).last(),
+            $firstDataset = this.$( '.unpaired-columns .reverse-column .dataset'
).first();
+        if( !$firstDataset.size() ){ return; }
+        var ucRight = $unpairedColumns.offset().left + $unpairedColumns.outerWidth(),
+            dsRight = $firstDataset.offset().left + $firstDataset.outerWidth(),
+            rightDiff = Math.floor( ucRight ) - Math.floor( dsRight );
+        //this.debug( 'rightDiff:', ucRight, '-', dsRight, '=',
rightDiff );
+        this.$( '.unpaired-columns .forward-column' )
+            .css( 'margin-left', ( rightDiff > 0 )? rightDiff: 0 );
+    },
 
     /** render the paired section and update counts of paired datasets */
     _renderPaired : function( speed, callback ){
@@ -907,6 +928,7 @@
         'click .paired-column-title'                :
'_clickShowOnlyPaired',
         'mousedown .flexible-partition-drag'        :
'_startPartitionDrag',
         // paired
+        'click .paired-columns .dataset.paired'     : 'selectPair',
         'click .paired-columns .pair-name'          : '_clickPairName',
         'click .unpair-btn'                         : '_clickUnpair',
 
@@ -965,28 +987,23 @@
             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.$( '.paired-columns' ).show( speed ).css( 'flex', '1 0
auto' );
         this.unpairedPanelHidden = true;
+        this.pairedPanelHidden = false;
+        this._renderMiddle( speed, callback );
     },
     /** hide paired, show unpaired */
     hidePaired : function( speed, callback ){
-        speed = speed || 0;
-        this.$( '.unpaired-columns' ).show( speed ).css( 'flex', '1 0
auto' );
-        //this.$( '.unpaired-filter' ).show( speed );
-        this.$( '.paired-columns' ).hide( speed, callback );
+        this.unpairedPanelHidden = false;
         this.pairedPanelHidden = true;
+        this._renderMiddle( speed, callback );
     },
     /** 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 );
+        this._renderMiddle( speed, callback );
         return this;
     },
 
@@ -1148,6 +1165,7 @@
                 //creator.debug( 'mouseup triggered' );
                 $( 'body' ).trigger( 'mouseup' );
             }
+            creator._adjUnpairedOnScrollbar();
             startingY += offset;
         }
         $( 'body' ).mousemove( trackMouse );
@@ -1165,29 +1183,37 @@
         unpairedHi = Math.max( 10, unpairedHi + adj );
         pairedHi = pairedHi - adj;
 
-        //TODO: seems like shouldn't need this (it should be part of the
hide/show/splitView)
-        if( unpairedHi <= 10 ){
-            if( !this.unpairedPanelHidden ){
+//TODO: seems like shouldn't need this (it should be part of the
hide/show/splitView)
+        var movingUpwards = adj < 0;
+        // when the divider gets close to the top - lock into hiding the unpaired
section
+        if( movingUpwards ){
+            if( this.unpairedPanelHidden ){
+                return false;
+            } else if( unpairedHi <= 10 ){
                 this.hideUnpaired();
                 return false;
             }
-
-        } else if( this.unpairedPanelHidden ){
-            $unpaired.show();
-            this.unpairedPanelHidden = false;
+        } else {
+            if( this.unpairedPanelHidden ){
+                $unpaired.show();
+                this.unpairedPanelHidden = false;
+            }
         }
 
         // when the divider gets close to the bottom - lock into hiding the paired
section
-        if( pairedHi <= 15 ){
-            if( !this.pairedPanelHidden ){
+        if( !movingUpwards ){
+            if( this.pairedPanelHidden ){
+                return false;
+            } else if( pairedHi <= 15 ){
                 this.hidePaired();
-                if( pairedHi < 5 ){ return false; }
+                return false;
             }
 
-        // when the divider gets close to the bottom and the paired section is hidden
-        } else if( this.pairedPanelHidden ){
-            $paired.show();
-            this.pairedPanelHidden = false;
+        } else {
+            if( this.pairedPanelHidden ){
+                $paired.show();
+                this.pairedPanelHidden = false;
+            }
         }
 
         $unpaired.css({
@@ -1198,8 +1224,14 @@
     },
 
     // ........................................................................ paired
+    /** select a pair when clicked */
+    selectPair : function( ev ){
+        $( ev.currentTarget ).toggleClass( 'selected' );
+    },
+
     /** rename a pair when the pair name is clicked */
     _clickPairName : function( ev ){
+        ev.stopPropagation();
         var $control = $( ev.currentTarget ),
             pair = this.paired[ $control.parent().index() ],
             response = prompt( 'Enter a new name for the pair:', pair.name );

diff -r 5a7a7003fbc3bc8f9d56f18a8d4b8f2d5b28fe42 -r
a66a80701913bb99e8abd12235c1ca82dc508f57
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","mvc/base-mvc","utils/localization"],function(g,a,d){var
f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset
paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).html(_.template(['<span
class="forward-dataset-name flex-column"><%= pair.forward.name
%></span>','<span class="pair-name flex-column"><%=
pair.name %></span>','<span class="reverse-dataset-name
flex-column"><%= pair.reverse.name
%></span>'].join(""),{pair:this.pair})).addClass("flex-column-container");return
this}});var
e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator
flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},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()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return
naturalSort(j.name,i.name)});return
h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return
this.initialList},_splitByFilters:function(j){var
i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var
h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new
RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var
h=function(j,l){if(j===l){return j}var
k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return
h(j,k)}else{if(m>0){return
h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return
k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(h){h=h||this.strategy;this.simpleAutoPair();return
this[h].call(this)},simpleAutoPair:function(){var
n=0,l,r=this._splitByFilters(),h=r[0],q=r[1],p,s,k=false;while(n<h.length){var
m=h[n];p=m.name.replace(this.filters[0],"");k=false;for(l=0;l<q.length;l++){var
o=q[l];s=o.name.replace(this.filters[1],"");if(m!==o&&p===s){k=true;this._pair(h.splice(n,1)[0],q.splice(l,1)[0],{silent:true});break}}if(!k){n+=1}}},autoPairLevenshtein:function(){var
o=0,m,t=this._splitByFilters(),h=t[0],r=t[1],q,v,k,s,l;while(o<h.length){var
n=h[o];q=n.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(m=0;m<r.length;m++){var
p=r[m];v=p.name.replace(this.filters[1],"");if(n!==p){if(q===v){s=m;l=0;break}k=levenshteinDistance(q,v);if(k<l){s=m;l=k}}}var
u=1-(l/(Math.max(q.length,v.length)));if(u>=this.matchPercentage){this._pair(h.splice(o,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{o+=1}}},autoPairLCSs:function(){var
m=0,k,t=this._splitByFilters(),h=t[0],r=t[1],q,w,v,s,o;if(!h.length||!r.length){return}while(m<h.length){var
l=h[m];q=l.name.replace(this.filters[0],"");o=0;for(k=0;k<r.length;k++){var
p=r[k];w=p.name.replace(this.filters[1],"");if(l!==p){if(q===w){s=k;o=q.length;break}var
n=this._naiveStartingAndEndingLCS(q,w);v=n.length;if(v>o){s=k;o=v}}}var
u=o/(Math.min(q.length,w.length));if(u>=this.matchPercentage){this._pair(h.splice(m,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{m+=1}}},_naiveStartingAndEndingLCS:function(m,k){var
n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return
m}if(l===k.length){return
k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return
n+o},_pair:function(j,h,i){i=i||{};var
k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return
k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad
pairing:
"+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var
i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var
l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" &
"+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair:
"+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return
i},unpairAll:function(){var
h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var
j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var
h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return
j._pairToJSON(k)})};return
jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof
j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var
i=d("An error occurred while creating this
collection");if(k){if(k.readyState===0&&k.status===0){i+=":
"+d("Galaxy could not be reached and may be updating.")+d(" Try again
in a few minutes.")}else{if(k.responseJSON){i+="<br
/><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=":
"+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();return
this},_renderHeader:function(i,j){var
h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return
h},_renderFilters:function(){return this.$(".forward-column .column-header
input").val(this.filters[0]).add(this.$(".reverse-column .column-header
input").val(this.filters[1]))},_renderMiddle:function(i,j){var
h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return
h},_renderUnpaired:function(m,n){var
k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column
.title").text([j[0].length,d("unpaired forward")].join("
"));this.$(".forward-column
.unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column
.title").text([j[1].length,d("unpaired reverse")].join("
"));this.$(".reverse-column
.unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns
.column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return
k._renderUnpairedDataset(p)});l=j[0].map(function(o){return
k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns
.forward-column .column-datasets").append(l).add(this.$(".unpaired-columns
.paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns
.reverse-column
.column-datasets").append(i))},_renderUnpairedDisplayStr:function(h){return["(",h,"
",d("filtered
out"),")"].join("")},_renderUnpairedDataset:function(h){return
$("<li/>").attr("id","dataset-"+h.id).addClass("dataset
unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return
$("<li/>").addClass("dataset
unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair
these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div
class="empty-message"></div>').text("("+d("no
remaining unpaired datasets")+")");this.$(".unpaired-columns
.paired-column .column-datasets").empty().prepend(h);return
h},_renderUnpairedNotShown:function(){var h=$('<div
class="empty-message"></div>').text("("+d("no
datasets were found matching the current
filters")+")");this.$(".unpaired-columns .paired-column
.column-datasets").empty().prepend(h);return
h},_renderPaired:function(i,j){this.$(".paired-column-title
.title").text([this.paired.length,d("paired")].join("
"));this.$(".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 h=this;this.paired.forEach(function(m,k){var l=new
f({pair:m});h.$(".paired-columns
.column-datasets").append(l.render().$el).append(['<button
class="unpair-btn">','<span class="fa fa-unlink"
title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var
h=$('<div
class="empty-message"></div>').text("("+d("no paired
datasets yet")+")");this.$(".paired-columns
.column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var
h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof
this.oncancel==="function"){this.$(".cancel-create.btn").show()}return
h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content
i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0
)")},_chooseFiltersPopover:function(h){function i(l,k){return['<button
class="filter-choice btn" ','data-forward="',l,'"
data-reverse="',k,'">',d("Forward"),":
",l,", ",d("Reverse"),":
",k,"</button>"].join("")}var j=$(_.template(['<div
class="choose-filters">','<div
class="help">',d("Choose from the following filters to change which
unpaired reads are shown in the
display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""),{}));return
this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var
j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){this._renderUnpaired();this._renderPaired();this.splitView()});this.on("filter-change",function(){this.filters=[this.$(".forward-unpaired-filter
input").val(),this.$(".reverse-unpaired-filter
input").val()];this._renderFilters();this._renderUnpaired()});this.on("autopair",function(){this._renderUnpaired();this._renderPaired();var
h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+"
"+d("pairs created");if(!this.unpaired.length){h+=":
"+d("all datasets have been successfully
paired");this.hideUnpaired()}}else{h=d("Could not automatically create any pairs
from the given dataset names")}this._showAlert(h,i)});return
this},events:{"click .more-help":"_clickMoreHelp","click
.less-help":"_clickLessHelp","click .header .alert
button":"_hideAlert","click .forward-column
.column-title":"_clickShowOnlyUnpaired","click .reverse-column
.column-title":"_clickShowOnlyUnpaired","click
.unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter
input":function(h){this.trigger("filter-change")},"focus
.forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click
.autopair-link":"_clickAutopair","click .choose-filters
.filter-choice":"_clickFilterChoice","click
.clear-filters-link":"_clearFilters","change .reverse-unpaired-filter
input":function(h){this.trigger("filter-change")},"focus
.reverse-unpaired-filter input":function(h){$(h.currentTarget).select()},"click
.forward-column .dataset.unpaired":"_clickUnpairedDataset","click
.reverse-column .dataset.unpaired":"_clickUnpairedDataset","click
.paired-column .dataset.unpaired":"_clickPairRow","click
.unpaired-columns":"clearSelectedUnpaired","mousedown
.unpaired-columns .dataset":"_mousedownUnpaired","click
.paired-column-title":"_clickShowOnlyPaired","mousedown
.flexible-partition-drag":"_startPartitionDrag","click .paired-columns
.pair-name":"_clickPairName","click
.unpair-btn":"_clickUnpair","change
.remove-extensions":function(h){this.toggleExtensions()},"change
.collection-name":"_changeName","click
.cancel-create":function(h){if(typeof
this.oncancel==="function"){this.oncancel.call(this)}},"click
.create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header
.alert").attr("class","alert
alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header
.alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){h=h||0;this.$(".unpaired-columns").hide(h,i);this.$(".paired-columns").show(h).css("flex","1
0
auto");this.unpairedPanelHidden=true},hidePaired:function(h,i){h=h||0;this.$(".unpaired-columns").show(h).css("flex","1
0
auto");this.$(".paired-columns").hide(h,i);this.pairedPanelHidden=true},splitView:function(h,i){h=h||0;this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h);return
this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(i){var
h=this.autoPair();this.trigger("autopair",h)},_clickFilterChoice:function(i){var
h=$(i.currentTarget);this.$(".forward-unpaired-filter
input").val(h.data("forward"));this.$(".reverse-unpaired-filter
input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter
input").val("");this.$(".reverse-unpaired-filter
input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return
this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var
k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return
j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return
j},pairAllSelected:function(i){i=i||{};var
j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column
.dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns
.reverse-column
.dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return
l},clearSelectedUnpaired:function(){this.$(".unpaired-columns
.dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var
i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var
k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column
.dataset").eq(k).data("dataset"),h=$(".unpaired-columns
.reverse-column
.dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var
h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function
k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function
j(m){var
n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var
h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;if(k<=10){if(!this.unpairedPanelHidden){this.hideUnpaired();return
false}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(l<=15){if(!this.pairedPanelHidden){this.hidePaired();if(l<5){return
false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0
0 auto"});return true},_clickPairName:function(j){var
i=$(j.currentTarget),k=this.paired[i.parent().index()],h=prompt("Enter a new name for
the
pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var
h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},toggleExtensions:function(i){var
h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_getName:function(){return
_.escape(this.$(".collection-name").val())},_clickCreate:function(i){var
h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var
h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,":
->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div
class="header flex-row no-flex"></div>','<div
class="middle flex-row flex-row-container"></div>','<div
class="footer flex-row
no-flex">'].join("")),header:_.template(['<div
class="main-help well clear">','<a class="more-help"
href="javascript:void(0);">',d("More
help"),"</a>",'<div
class="help-content">','<a class="less-help"
href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div
class="alert alert-dismissable">','<button type="button"
class="close" data-dismiss="alert"
aria-hidden="true">&times;</button>','<span
class="alert-message"></span>',"</div>",'<div
class="column-headers vertically-spaced
flex-column-container">','<div class="forward-column flex-column
column">','<div class="column-header">','<div
class="column-title">','<span
class="title">',d("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="',d("Filter this list"),'"
/>',"</div>","</div>","</div>",'<div
class="paired-column flex-column no-flex column">','<div
class="column-header">','<a class="choose-filters-link"
href="javascript:void(0)">',d("Choose
filters"),"</a>",'<a class="clear-filters-link"
href="javascript:void(0);">',d("Clear
filters"),"</a><br />",'<a
class="autopair-link"
href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div
class="reverse-column flex-column column">','<div
class="column-header">','<div
class="column-title">','<span
class="title">',d("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="',d("Filter this list"),'"
/>',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div
class="unpaired-columns flex-column-container scroll-container
flex-row">','<div class="forward-column flex-column
column">','<ol
class="column-datasets"></ol>',"</div>",'<div
class="paired-column flex-column no-flex 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" title="',d("Drag to
change"),'"></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);">',d("Unpair
all"),"</a>","</div>","</div>",'<div
class="paired-columns flex-column-container scroll-container
flex-row">','<ol
class="column-datasets"></ol>',"</div>"].join("")),footer:_.template(['<div
class="attributes clear">','<div
class="clear">','<label class="remove-extensions-prompt
pull-right">',d("Remove file extensions from pair
names"),"?",'<input class="remove-extensions pull-right"
type="checkbox"
/>',"</label>","</div>",'<div
class="clear">','<input class="collection-name form-control
pull-right" ','placeholder="',d("Enter a name for your new
list"),'" />','<div class="collection-name-prompt
pull-right">',d("Name"),":</div>","</div>","</div>",'<div
class="actions clear vertically-spaced">','<div
class="other-options pull-left">','<button
class="cancel-create btn"
tabindex="-1">',d("Cancel"),"</button>",'<div
class="create-other btn-group dropup">','<button class="btn
btn-default dropdown-toggle" data-toggle="dropdown">',d("Create
a different kind of collection"),' <span
class="caret"></span>',"</button>",'<ul
class="dropdown-menu" role="menu">','<li><a
href="#">',d("Create a <i>single</i>
pair"),"</a></li>",'<li><a
href="#">',d("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">',d("Create
list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",d(["Collections
of paired datasets are ordered lists of dataset pairs (often forward and reverse reads).
","These collections can be passed to tools and workflows in order to have
analyses done on each member of ","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>",d(['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>",d(["<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>Entering regular expressions
to match dataset names. See: ",'<a
href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/...
target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>.
',"Note: forward slashes (\\) are not
needed.","</li>","<li>Clearing the filters by clicking the
",'<i data-target=".clear-filters-link">"Clear filters"
link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["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>",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
h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var
l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return
this}})}());var b=function
c(j,h){h=_.defaults(h||{},{datasets:j,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 i=new
e(h).render();Galaxy.modal.show({title:"Create a collection of paired
datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return
i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}});
\ No newline at end of file
+define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var
f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset
paired",initialize:function(h){this.pair=h.pair||{}},render:function(){this.$el.attr("draggable",true).html(_.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(""),{pair:this.pair})).addClass("flex-column-container");return
this}});var
e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator
flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this._dataSetUp();this._setUpBehaviors()},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()}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(h){h.sort(function(j,i){return
naturalSort(j.name,i.name)});return
h},_ensureIds:function(){this.initialList.forEach(function(h){if(!h.hasOwnProperty("id")){h.id=_.uniqueId()}});return
this.initialList},_splitByFilters:function(j){var
i=[],h=[];this.unpaired.forEach(function(k){if(this._filterFwdFn(k)){i.push(k)}if(this._filterRevFn(k)){h.push(k)}}.bind(this));return[i,h]},_filterFwdFn:function(i){var
h=new RegExp(this.filters[0]);return h.test(i.name)},_filterRevFn:function(i){var h=new
RegExp(this.filters[1]);return h.test(i.name)},_addToUnpaired:function(i){var
h=function(j,l){if(j===l){return j}var
k=Math.floor((l-j)/2)+j,m=naturalSort(i.name,this.unpaired[k].name);if(m<0){return
h(j,k)}else{if(m>0){return
h(k+1,l)}}while(this.unpaired[k]&&this.unpaired[k].name===i.name){k++}return
k}.bind(this);this.unpaired.splice(h(0,this.unpaired.length),0,i)},autoPair:function(h){h=h||this.strategy;this.simpleAutoPair();return
this[h].call(this)},simpleAutoPair:function(){var
n=0,l,r=this._splitByFilters(),h=r[0],q=r[1],p,s,k=false;while(n<h.length){var
m=h[n];p=m.name.replace(this.filters[0],"");k=false;for(l=0;l<q.length;l++){var
o=q[l];s=o.name.replace(this.filters[1],"");if(m!==o&&p===s){k=true;this._pair(h.splice(n,1)[0],q.splice(l,1)[0],{silent:true});break}}if(!k){n+=1}}},autoPairLevenshtein:function(){var
o=0,m,t=this._splitByFilters(),h=t[0],r=t[1],q,v,k,s,l;while(o<h.length){var
n=h[o];q=n.name.replace(this.filters[0],"");l=Number.MAX_VALUE;for(m=0;m<r.length;m++){var
p=r[m];v=p.name.replace(this.filters[1],"");if(n!==p){if(q===v){s=m;l=0;break}k=levenshteinDistance(q,v);if(k<l){s=m;l=k}}}var
u=1-(l/(Math.max(q.length,v.length)));if(u>=this.matchPercentage){this._pair(h.splice(o,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{o+=1}}},autoPairLCSs:function(){var
m=0,k,t=this._splitByFilters(),h=t[0],r=t[1],q,w,v,s,o;if(!h.length||!r.length){return}while(m<h.length){var
l=h[m];q=l.name.replace(this.filters[0],"");o=0;for(k=0;k<r.length;k++){var
p=r[k];w=p.name.replace(this.filters[1],"");if(l!==p){if(q===w){s=k;o=q.length;break}var
n=this._naiveStartingAndEndingLCS(q,w);v=n.length;if(v>o){s=k;o=v}}}var
u=o/(Math.min(q.length,w.length));if(u>=this.matchPercentage){this._pair(h.splice(m,1)[0],r.splice(s,1)[0],{silent:true});if(h.length<=0||r.length<=0){return}}else{m+=1}}},_naiveStartingAndEndingLCS:function(m,k){var
n="",o="",l=0,h=0;while(l<m.length&&l<k.length){if(m[l]!==k[l]){break}n+=m[l];l+=1}if(l===m.length){return
m}if(l===k.length){return
k}l=(m.length-1);h=(k.length-1);while(l>=0&&h>=0){if(m[l]!==k[h]){break}o=[m[l],o].join("");l-=1;h-=1}return
n+o},_pair:function(j,h,i){i=i||{};var
k=this._createPair(j,h,i.name);this.paired.push(k);this.unpaired=_.without(this.unpaired,j,h);if(!i.silent){this.trigger("pair:new",k)}return
k},_createPair:function(j,h,i){if(!(j&&h)||(j===h)){throw new Error("Bad
pairing:
"+[JSON.stringify(j),JSON.stringify(h)])}i=i||this._guessNameForPair(j,h);return{forward:j,name:i,reverse:h}},_guessNameForPair:function(j,h,k){k=(k!==undefined)?(k):(this.removeExtensions);var
i=this._naiveStartingAndEndingLCS(j.name.replace(this.filters[0],""),h.name.replace(this.filters[1],""));if(k){var
l=i.lastIndexOf(".");if(l>0){i=i.slice(0,l)}}return i||(j.name+" &
"+h.name)},_unpair:function(i,h){h=h||{};if(!i){throw new Error("Bad pair:
"+JSON.stringify(i))}this.paired=_.without(this.paired,i);this._addToUnpaired(i.forward);this._addToUnpaired(i.reverse);if(!h.silent){this.trigger("pair:unpair",[i])}return
i},unpairAll:function(){var
h=[];while(this.paired.length){h.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",h)},_pairToJSON:function(h){return{collection_type:"paired",src:"new_collection",name:h.name,element_identifiers:[{name:"forward",id:h.forward.id,src:"hda"},{name:"reverse",id:h.reverse.id,src:"hda"}]}},createList:function(){var
j=this,i;if(j.historyId){i="/api/histories/"+this.historyId+"/contents/dataset_collections"}var
h={type:"dataset_collection",collection_type:"list:paired",name:_.escape(j.$(".collection-name").val()),element_identifiers:j.paired.map(function(k){return
j._pairToJSON(k)})};return
jQuery.ajax(i,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(h)}).fail(function(m,k,l){j._ajaxErrHandler(m,k,l)}).done(function(k,l,m){j.trigger("collection:created",k,l,m);if(typeof
j.oncreate==="function"){j.oncreate.call(this,k,l,m)}})},_ajaxErrHandler:function(k,h,j){this.error(k,h,j);var
i=d("An error occurred while creating this
collection");if(k){if(k.readyState===0&&k.status===0){i+=":
"+d("Galaxy could not be reached and may be updating.")+d(" Try again
in a few minutes.")}else{if(k.responseJSON){i+="<br
/><pre>"+JSON.stringify(k.responseJSON)+"</pre>"}else{i+=":
"+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();return
this},_renderHeader:function(i,j){var
h=this.$(".header").empty().html(e.templates.header()).find(".help-content").prepend($(e.templates.helpContent()));this._renderFilters();return
h},_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(i,j){var
h=this.$(".middle").empty().html(e.templates.middle());if(this.unpairedPanelHidden){this.$(".unpaired-columns").hide()}else{if(this.pairedPanelHidden){this.$(".paired-columns").hide()}}this._renderUnpaired();this._renderPaired();return
h},_renderUnpaired:function(m,n){var
k=this,l,i,h=[],j=this._splitByFilters();this.$(".forward-column
.title").text([j[0].length,d("unpaired forward")].join("
"));this.$(".forward-column
.unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[0].length));this.$(".reverse-column
.title").text([j[1].length,d("unpaired reverse")].join("
"));this.$(".reverse-column
.unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-j[1].length));this.$(".unpaired-columns
.column-datasets").empty();this.$(".autopair-link").toggle(this.unpaired.length!==0);if(this.unpaired.length===0){this._renderUnpairedEmpty();return}i=j[1].map(function(p,o){if((j[0][o]!==undefined)&&(j[0][o]!==p)){h.push(k._renderPairButton())}return
k._renderUnpairedDataset(p)});l=j[0].map(function(o){return
k._renderUnpairedDataset(o)});if(!l.length&&!i.length){this._renderUnpairedNotShown();return}this.$(".unpaired-columns
.forward-column .column-datasets").append(l).add(this.$(".unpaired-columns
.paired-column .column-datasets").append(h)).add(this.$(".unpaired-columns
.reverse-column
.column-datasets").append(i));this._adjUnpairedOnScrollbar()},_renderUnpairedDisplayStr:function(h){return["(",h,"
",d("filtered
out"),")"].join("")},_renderUnpairedDataset:function(h){return
$("<li/>").attr("id","dataset-"+h.id).addClass("dataset
unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("<span/>").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return
$("<li/>").addClass("dataset
unpaired").append($("<span/>").addClass("dataset-name").text(d("Pair
these datasets")))},_renderUnpairedEmpty:function(){var h=$('<div
class="empty-message"></div>').text("("+d("no
remaining unpaired datasets")+")");this.$(".unpaired-columns
.paired-column .column-datasets").empty().prepend(h);return
h},_renderUnpairedNotShown:function(){var h=$('<div
class="empty-message"></div>').text("("+d("no
datasets were found matching the current
filters")+")");this.$(".unpaired-columns .paired-column
.column-datasets").empty().prepend(h);return
h},_adjUnpairedOnScrollbar:function(){var
k=this.$(".unpaired-columns").last(),l=this.$(".unpaired-columns
.reverse-column .dataset").first();if(!l.size()){return}var
h=k.offset().left+k.outerWidth(),j=l.offset().left+l.outerWidth(),i=Math.floor(h)-Math.floor(j);this.$(".unpaired-columns
.forward-column").css("margin-left",(i>0)?i:0)},_renderPaired:function(i,j){this.$(".paired-column-title
.title").text([this.paired.length,d("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.$(".paired-columns
.column-datasets").empty();var h=this;this.paired.forEach(function(m,k){var l=new
f({pair:m});h.$(".paired-columns
.column-datasets").append(l.render().$el).append(['<button
class="unpair-btn">','<span class="fa fa-unlink"
title="',d("Unpair"),'"></span>',"</button>"].join(""))})},_renderPairedEmpty:function(){var
h=$('<div
class="empty-message"></div>').text("("+d("no paired
datasets yet")+")");this.$(".paired-columns
.column-datasets").empty().prepend(h);return h},_renderFooter:function(i,j){var
h=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof
this.oncancel==="function"){this.$(".cancel-create.btn").show()}return
h},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content
i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0
)")},_chooseFiltersPopover:function(h){function i(l,k){return['<button
class="filter-choice btn" ','data-forward="',l,'"
data-reverse="',k,'">',d("Forward"),":
",l,", ",d("Reverse"),":
",k,"</button>"].join("")}var j=$(_.template(['<div
class="choose-filters">','<div
class="help">',d("Choose from the following filters to change which
unpaired reads are shown in the
display"),":</div>",i("_1","_2"),i("_R1","_R2"),"</div>"].join(""),{}));return
this.$(h).popover({container:".collection-creator",placement:"bottom",html:true,content:j})},_validationWarning:function(i,h){var
j="validation-warning";if(i==="name"){i=this.$(".collection-name").add(this.$(".collection-name-prompt"));this.$(".collection-name").focus().select()}if(h){i=i||this.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(h){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
h,i=null;if(this.paired.length){i="alert-success";h=this.paired.length+"
"+d("pairs created");if(!this.unpaired.length){h+=":
"+d("all datasets have been successfully
paired");this.hideUnpaired()}}else{h=d("Could not automatically create any pairs
from the given dataset names")}this._showAlert(h,i)});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(h){this.trigger("filter-change")},"focus
.forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click
.autopair-link":"_clickAutopair","click .choose-filters
.filter-choice":"_clickFilterChoice","click
.clear-filters-link":"_clearFilters","change .reverse-unpaired-filter
input":function(h){this.trigger("filter-change")},"focus
.reverse-unpaired-filter input":function(h){$(h.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
.pair-name":"_clickPairName","click
.unpair-btn":"_clickUnpair","change
.remove-extensions":function(h){this.toggleExtensions()},"change
.collection-name":"_changeName","click
.cancel-create":function(h){if(typeof
this.oncancel==="function"){this.oncancel.call(this)}},"click
.create-collection":"_clickCreate"},_clickMoreHelp:function(h){this.$(".main-help").addClass("expanded");this.$(".more-help").hide()},_clickLessHelp:function(h){this.$(".main-help").removeClass("expanded");this.$(".more-help").show()},_showAlert:function(i,h){h=h||"alert-danger";this.$(".main-help").hide();this.$(".header
.alert").attr("class","alert
alert-dismissable").addClass(h).show().find(".alert-message").html(i)},_hideAlert:function(h){this.$(".main-help").show();this.$(".header
.alert").hide()},_clickShowOnlyUnpaired:function(h){if(this.$(".paired-columns").is(":visible")){this.hidePaired()}else{this.splitView()}},_clickShowOnlyPaired:function(h){if(this.$(".unpaired-columns").is(":visible")){this.hideUnpaired()}else{this.splitView()}},hideUnpaired:function(h,i){this.unpairedPanelHidden=true;this.pairedPanelHidden=false;this._renderMiddle(h,i)},hidePaired:function(h,i){this.unpairedPanelHidden=false;this.pairedPanelHidden=true;this._renderMiddle(h,i)},splitView:function(h,i){this.unpairedPanelHidden=this.pairedPanelHidden=false;this._renderMiddle(h,i);return
this},_clickUnpairAll:function(h){this.unpairAll()},_clickAutopair:function(i){var
h=this.autoPair();this.trigger("autopair",h)},_clickFilterChoice:function(i){var
h=$(i.currentTarget);this.$(".forward-unpaired-filter
input").val(h.data("forward"));this.$(".reverse-unpaired-filter
input").val(h.data("reverse"));this._hideChooseFilters();this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide");this.$(".popover").css("display","none")},_clearFilters:function(h){this.$(".forward-unpaired-filter
input").val("");this.$(".reverse-unpaired-filter
input").val("");this.trigger("filter-change")},_clickUnpairedDataset:function(h){h.stopPropagation();return
this.toggleSelectUnpaired($(h.currentTarget))},toggleSelectUnpaired:function(j,i){i=i||{};var
k=j.data("dataset"),h=i.force!==undefined?i.force:!j.hasClass("selected");if(!j.size()||k===undefined){return
j}if(h){j.addClass("selected");if(!i.waitToPair){this.pairAllSelected()}}else{j.removeClass("selected")}return
j},pairAllSelected:function(i){i=i||{};var
j=this,k=[],h=[],l=[];j.$(".unpaired-columns .forward-column
.dataset.selected").each(function(){k.push($(this).data("dataset"))});j.$(".unpaired-columns
.reverse-column
.dataset.selected").each(function(){h.push($(this).data("dataset"))});k.length=h.length=Math.min(k.length,h.length);k.forEach(function(n,m){try{l.push(j._pair(n,h[m],{silent:true}))}catch(o){j.error(o)}});if(l.length&&!i.silent){this.trigger("pair:new",l)}return
l},clearSelectedUnpaired:function(){this.$(".unpaired-columns
.dataset.selected").removeClass("selected")},_mousedownUnpaired:function(j){if(j.shiftKey){var
i=this,h=$(j.target).addClass("selected"),k=function(l){i.$(l.target).filter(".dataset").addClass("selected")};h.parent().on("mousemove",k);$(document).one("mouseup",function(l){h.parent().off("mousemove",k);i.pairAllSelected()})}},_clickPairRow:function(j){var
k=$(j.currentTarget).index(),i=$(".unpaired-columns .forward-column
.dataset").eq(k).data("dataset"),h=$(".unpaired-columns
.reverse-column
.dataset").eq(k).data("dataset");this._pair(i,h)},_startPartitionDrag:function(i){var
h=this,l=i.pageY;$("body").css("cursor","ns-resize");h.$(".flexible-partition-drag").css("color","black");function
k(m){h.$(".flexible-partition-drag").css("color","");$("body").css("cursor","").unbind("mousemove",j)}function
j(m){var
n=m.pageY-l;if(!h.adjPartition(n)){$("body").trigger("mouseup")}h._adjUnpairedOnScrollbar();l+=n}$("body").mousemove(j);$("body").one("mouseup",k)},adjPartition:function(i){var
h=this.$(".unpaired-columns"),j=this.$(".paired-columns"),k=parseInt(h.css("height"),10),l=parseInt(j.css("height"),10);k=Math.max(10,k+i);l=l-i;var
m=i<0;if(m){if(this.unpairedPanelHidden){return
false}else{if(k<=10){this.hideUnpaired();return
false}}}else{if(this.unpairedPanelHidden){h.show();this.unpairedPanelHidden=false}}if(!m){if(this.pairedPanelHidden){return
false}else{if(l<=15){this.hidePaired();return
false}}}else{if(this.pairedPanelHidden){j.show();this.pairedPanelHidden=false}}h.css({height:k+"px",flex:"0
0 auto"});return
true},selectPair:function(h){$(h.currentTarget).toggleClass("selected")},_clickPairName:function(j){j.stopPropagation();var
i=$(j.currentTarget),k=this.paired[i.parent().index()],h=prompt("Enter a new name for
the
pair:",k.name);if(h){k.name=h;k.customizedName=true;i.text(k.name)}},_clickUnpair:function(i){var
h=Math.floor($(i.currentTarget).index()/2);this._unpair(this.paired[h])},toggleExtensions:function(i){var
h=this;h.removeExtensions=(i!==undefined)?(i):(!h.removeExtensions);_.each(h.paired,function(j){if(j.customizedName){return}j.name=h._guessNameForPair(j.forward,j.reverse)});h._renderPaired();h._renderFooter()},_changeName:function(h){this._validationWarning("name",!!this._getName())},_getName:function(){return
_.escape(this.$(".collection-name").val())},_clickCreate:function(i){var
h=this._getName();if(!h){this._validationWarning("name")}else{this.createList()}},_printList:function(i){var
h=this;_.each(i,function(j){if(i===h.paired){h._printPair(j)}else{}})},_printPair:function(h){this.debug(h.forward.name,h.reverse.name,":
->",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['<div
class="header flex-row no-flex"></div>','<div
class="middle flex-row flex-row-container"></div>','<div
class="footer flex-row
no-flex">'].join("")),header:_.template(['<div
class="main-help well clear">','<a class="more-help"
href="javascript:void(0);">',d("More
help"),"</a>",'<div
class="help-content">','<a class="less-help"
href="javascript:void(0);">',d("Less"),"</a>","</div>","</div>",'<div
class="alert alert-dismissable">','<button type="button"
class="close" data-dismiss="alert"
aria-hidden="true">&times;</button>','<span
class="alert-message"></span>',"</div>",'<div
class="column-headers vertically-spaced
flex-column-container">','<div class="forward-column flex-column
column">','<div class="column-header">','<div
class="column-title">','<span
class="title">',d("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="',d("Filter this list"),'"
/>',"</div>","</div>","</div>",'<div
class="paired-column flex-column no-flex column">','<div
class="column-header">','<a class="choose-filters-link"
href="javascript:void(0)">',d("Choose
filters"),"</a>",'<a class="clear-filters-link"
href="javascript:void(0);">',d("Clear
filters"),"</a><br />",'<a
class="autopair-link"
href="javascript:void(0);">',d("Auto-pair"),"</a>","</div>","</div>",'<div
class="reverse-column flex-column column">','<div
class="column-header">','<div
class="column-title">','<span
class="title">',d("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="',d("Filter this list"),'"
/>',"</div>","</div>","</div>","</div>"].join("")),middle:_.template(['<div
class="unpaired-columns flex-column-container scroll-container
flex-row">','<div class="forward-column flex-column
column">','<ol
class="column-datasets"></ol>',"</div>",'<div
class="paired-column flex-column no-flex 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" title="',d("Drag to
change"),'"></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);">',d("Unpair
all"),"</a>","</div>","</div>",'<div
class="paired-columns flex-column-container scroll-container
flex-row">','<ol
class="column-datasets"></ol>',"</div>"].join("")),footer:_.template(['<div
class="attributes clear">','<div
class="clear">','<label class="remove-extensions-prompt
pull-right">',d("Remove file extensions from pair
names"),"?",'<input class="remove-extensions pull-right"
type="checkbox"
/>',"</label>","</div>",'<div
class="clear">','<input class="collection-name form-control
pull-right" ','placeholder="',d("Enter a name for your new
list"),'" />','<div class="collection-name-prompt
pull-right">',d("Name"),":</div>","</div>","</div>",'<div
class="actions clear vertically-spaced">','<div
class="other-options pull-left">','<button
class="cancel-create btn"
tabindex="-1">',d("Cancel"),"</button>",'<div
class="create-other btn-group dropup">','<button class="btn
btn-default dropdown-toggle" data-toggle="dropdown">',d("Create
a different kind of collection"),' <span
class="caret"></span>',"</button>",'<ul
class="dropdown-menu" role="menu">','<li><a
href="#">',d("Create a <i>single</i>
pair"),"</a></li>",'<li><a
href="#">',d("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">',d("Create
list"),"</button>","</div>","</div>"].join("")),helpContent:_.template(["<p>",d(["Collections
of paired datasets are ordered lists of dataset pairs (often forward and reverse reads).
","These collections can be passed to tools and workflows in order to have
analyses done on each member of ","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>",d(['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>",d(["<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>Entering regular expressions
to match dataset names. See: ",'<a
href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/...
target="_blank">MDN\'s JavaScript Regular Expression Tutorial</a>.
',"Note: forward slashes (\\) are not
needed.","</li>","<li>Clearing the filters by clicking the
",'<i data-target=".clear-filters-link">"Clear filters"
link</i>.',"</li>","</ul>"].join("")),"</p>","<p>",d(["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>",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
h(j,i){j=j||"body";if(!this.size()){return this}$(this).each(function(){var
l=$(this),k=l.data("target");if(k){l.mouseover(function(m){$(k,j).css({background:i})}).mouseout(function(m){$(k).css({background:""})})}});return
this}})}());var b=function
c(j,h){h=_.defaults(h||{},{datasets:j,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 i=new
e(h).render();Galaxy.modal.show({title:"Create a collection of paired
datasets",body:i.$el,width:"80%",height:"800px",closing_events:true});window.PCC=i;return
i};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}});
\ No newline at end of file

diff -r 5a7a7003fbc3bc8f9d56f18a8d4b8f2d5b28fe42 -r
a66a80701913bb99e8abd12235c1ca82dc508f57 static/style/blue/base.css
--- a/static/style/blue/base.css
+++ b/static/style/blue/base.css
@@ -1851,12 +1851,16 @@
 .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 .unpaired-columns,.collection-creator
.paired-columns{height:0;border:1px solid lightgrey;border-width:1px 0 1px 0}
-.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}.collection-creator .column-datasets
.dataset:last-child{margin-bottom:4px}
-.collection-creator .unpaired-columns
.dataset.unpaired{margin-top:2px;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 .flex-bordered-vertically{height:0;border:1px solid
lightgrey;border-width:1px 0 1px 0}
+.collection-creator .column-datasets{list-style:none;overflow:hidden}.collection-creator
.column-datasets .dataset{height:32px;margin-top:2px;border:1px solid
lightgrey;border-radius:3px;padding:0 8px 0
8px;line-height:28px;cursor:pointer}.collection-creator .column-datasets
.dataset:last-of-type{margin-bottom:2px}
+.collection-creator .column-datasets .dataset.unpaired{border-color:grey}
+.collection-creator .column-datasets
.dataset.paired{margin-left:34px;margin-right:34px;border:2px solid
grey;background:#AFF1AF}.collection-creator .column-datasets .dataset.paired
span{display:inline-block;overflow:hidden}
+.collection-creator .column-datasets .dataset.paired
.forward-dataset-name{text-align:right;border-right:1px solid
grey;padding-right:8px}.collection-creator .column-datasets .dataset.paired
.forward-dataset-name:after{margin-left:8px;font-family:FontAwesome;content:'\f061'}
+.collection-creator .column-datasets .dataset.paired
.pair-name-column{text-align:center}.collection-creator .column-datasets .dataset.paired
.pair-name-column .pair-name:hover{text-decoration:underline}
+.collection-creator .column-datasets .dataset.paired
.reverse-dataset-name{border-left:1px solid grey;padding-left:8px}.collection-creator
.column-datasets .dataset.paired
.reverse-dataset-name:before{margin-right:8px;font-family:FontAwesome;content:'\f060'}
+.collection-creator .column-datasets .dataset:hover{border-color:black}
+.collection-creator .column-datasets
.dataset.selected{border-color:black;background:black;color:white}
+.collection-creator .unpaired-columns{height:0;border:1px solid
lightgrey;border-width:1px 0 1px 0}.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;line-height:2px;text-align:center;color:lightgrey}.collection-creator
.flexible-partition .flexible-partition-drag:before{content:'...'}
@@ -1864,13 +1868,8 @@
 .collection-creator .flexible-partition
.column-header{width:100%;text-align:center}.collection-creator .flexible-partition
.column-header .column-title{display:inline}
 .collection-creator .flexible-partition
.column-header>*:not(:last-child){margin-right:8px}
 .collection-creator .flexible-partition .column-header
.remove-extensions-link{display:none}
-.collection-creator .paired-columns
.column-datasets{width:100%;overflow:auto}.collection-creator .paired-columns
.column-datasets .dataset.paired{margin:0px 34px 2px 34px;border-radius:3px;border:2px
solid grey;background:#AFF1AF}.collection-creator .paired-columns .column-datasets
.dataset.paired:first-child{margin-top:2px}
-.collection-creator .paired-columns .column-datasets
.dataset.paired:hover,.collection-creator .paired-columns .column-datasets
.dataset.paired.emphasized{border-color:black}
-.collection-creator .paired-columns .column-datasets .dataset.paired
span{display:inline-block;overflow:hidden}
-.collection-creator .paired-columns .column-datasets .dataset.paired
.forward-dataset-name{text-align:right;border-right:1px solid
grey;padding-right:8px}.collection-creator .paired-columns .column-datasets
.dataset.paired
.forward-dataset-name:after{margin-left:8px;font-family:FontAwesome;content:'\f061'}
-.collection-creator .paired-columns .column-datasets .dataset.paired
.pair-name{display:inline-block;text-align:center}.collection-creator .paired-columns
.column-datasets .dataset.paired .pair-name:hover{text-decoration:underline}
-.collection-creator .paired-columns .column-datasets .dataset.paired
.reverse-dataset-name{display:inline-block;border-left:1px solid
grey;padding-left:8px}.collection-creator .paired-columns .column-datasets .dataset.paired
.reverse-dataset-name:before{margin-right:8px;font-family:FontAwesome;content:'\f060'}
-.collection-creator .paired-columns
.unpair-btn{float:right;margin-top:-34px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator
.paired-columns .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE}
+.collection-creator .paired-columns{height:0;border:1px solid lightgrey;border-width:1px
0 1px 0;margin-bottom:8px}.collection-creator .paired-columns
.column-datasets{width:100%;overflow:auto}
+.collection-creator .paired-columns
.unpair-btn{float:right;margin-top:-32px;width:31px;height:32px;border-color:transparent;background:transparent;font-size:120%}.collection-creator
.paired-columns .unpair-btn:hover{border-color:#BFBFBF;background:#DEDEDE}
 .collection-creator .paired-columns .empty-message{text-align:center}
 .collection-creator .footer{padding-bottom:8px}.collection-creator .footer .attributes
.remove-extensions-prompt{line-height:32px}.collection-creator .footer .attributes
.remove-extensions-prompt .remove-extensions{display:inline-block;width:24px;height:24px}
 .collection-creator .footer .attributes .collection-name-prompt{margin:5px 4px 0 0}

diff -r 5a7a7003fbc3bc8f9d56f18a8d4b8f2d5b28fe42 -r
a66a80701913bb99e8abd12235c1ca82dc508f57
static/style/src/less/ui/paired-collection-creator.less
--- a/static/style/src/less/ui/paired-collection-creator.less
+++ b/static/style/src/less/ui/paired-collection-creator.less
@@ -211,10 +211,9 @@
     }
 
     // ------------------------------------------------------------------------ middle
-    .middle {
-    }
-    .unpaired-columns,
-    .paired-columns {
+    // ---- all
+    // macro
+    .flex-bordered-vertically {
         // huh! - giving these any static height will pull them in
         height: 0;
         // NOT setting the above will give a full-height page
@@ -222,46 +221,80 @@
         border: 1px solid lightgrey;
         border-width: 1px 0 1px 0;
     }
-    // ------------------------------------------------------------------------ unpaired
-    .paired-columns {
-        margin-bottom: 8px;
-    }
 
-    // ------------------------------------------------------------------------ middle
-    // ---- all
     .column-datasets {
         list-style: none;
         overflow: hidden;
 
         .dataset {
             height: 32px;
-            margin-bottom: 2px;
+            margin-top: 2px;
+            &:last-of-type {
+                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 {
+                border-color: grey;
+            }
+
+            &.paired {
+                margin-left: 34px;
+                margin-right: 34px;
+                border: 2px solid grey;
+                background: #AFF1AF;
+
+                span {
+                    display: inline-block;
+                    overflow: hidden;
+                }
+                .forward-dataset-name {
+                    text-align: right;
+                    border-right: 1px solid grey;
+                    padding-right: 8px;
+                    &:after {
+                        margin-left: 8px;
+                        font-family: FontAwesome;
+                        content: '\f061';
+                    }
+                }
+                .pair-name-column {
+                    text-align: center;
+                    .pair-name:hover {
+                        text-decoration: underline;
+                    }
+                }
+                .reverse-dataset-name {
+                    border-left: 1px solid grey;
+                    padding-left: 8px;
+                    &:before {
+                        margin-right: 8px;
+                        font-family: FontAwesome;
+                        content: '\f060';
+                    }
+                }
+            }
+
+            &:hover {
+                border-color: black;
+            }
+
+            &.selected {
+                border-color: black;
+                background: black;
+                color: white;
             }
         }
     }
 
     // ---- unpaired
     .unpaired-columns {
-        .dataset.unpaired {
-            margin-top: 2px;
-            border-color: grey;
-            &:hover {
-                border-color: black;
-            }
-            &.selected {
-                border-color: black;
-                background: black;
-                color: white;
-            }
-        }
+        .flex-bordered-vertically;
+
         .forward-column {
             .dataset.unpaired {
                 margin-right: 32px;
@@ -319,62 +352,16 @@
 
     // ---- paired datasets
     .paired-columns {
+        .flex-bordered-vertically;
+        margin-bottom: 8px;
+
         .column-datasets {
             width: 100%;
             overflow: auto;
-
-            .dataset.paired {
-                &:first-child {
-                    margin-top: 2px;
-                }
-                margin: 0px 34px 2px 34px;
-
-                border-radius: 3px;
-                border: 2px solid grey;
-
-                background: #AFF1AF;
-
-                &:hover,
-                &.emphasized {
-                    border-color: black;
-                }
-
-                span {
-                    display: inline-block;
-                    overflow: hidden;
-                }
-                .forward-dataset-name {
-                    text-align: right;
-                    border-right: 1px solid grey;
-                    padding-right: 8px;
-                    &:after {
-                        margin-left: 8px;
-                        font-family: FontAwesome;
-                        content: '\f061';
-                    }
-                }
-                .pair-name {
-                    display: inline-block;
-                    text-align: center;
-                    &:hover {
-                        text-decoration: underline;
-                    }
-                }
-                .reverse-dataset-name {
-                    display: inline-block;
-                    border-left: 1px solid grey;
-                    padding-left: 8px;
-                    &:before {
-                        margin-right: 8px;
-                        font-family: FontAwesome;
-                        content: '\f060';
-                    }
-                }
-            }
         }
         .unpair-btn {
             float: right;
-            margin-top: -34px;
+            margin-top: -32px;
             width: 31px;
             height: 32px;
             //z-index: 1;

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

--

This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.


    

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010