diff --git a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js index 269650b427b..e4137a1db9f 100644 --- a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js @@ -568,7 +568,8 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte */ createList : function( name ){ var creator = this, - url = '/api/histories/' + this.historyId + '/contents/dataset_collections'; + root = ( window.Galaxy && Galaxy.options.root )? Galaxy.options.root : '/', + url = root + 'api/histories/' + this.historyId + '/contents/dataset_collections'; //TODO: use ListPairedCollection.create() var ajaxData = { diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 7653d1e90be..92006b3dc99 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -973,9 +973,10 @@ use_interactive = True # Very large metadata values can cause Galaxy crashes. This will allow # limiting the maximum metadata key size (in bytes used in memory, not the end -# result database value size) Galaxy will attempt to save with a dataset. 0 to -# disable this feature. 5000000 seems to be a reasonable size. -#max_metadata_value_size = 0 +# result database value size) Galaxy will attempt to save with a dataset. Use +# 0 to disable this feature. The default is 5MB, but as low as 1MB seems to be +# a reasonable size. +#max_metadata_value_size = 5242880 # If (for example) you run on a cluster and your datasets (by default, # database/files/) are mounted read-only, this option will override tool output diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 52c65ea9741..d8ef4f90a75 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -146,7 +146,7 @@ class Configuration( object ): self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) ) - self.max_metadata_value_size = int( kwargs.get( "max_metadata_value_size", 0 ) ) + self.max_metadata_value_size = int( kwargs.get( "max_metadata_value_size", 5242880 ) ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.normalize_remote_user_email = string_as_bool( kwargs.get( "normalize_remote_user_email", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) diff --git a/lib/galaxy/datatypes/metadata.py b/lib/galaxy/datatypes/metadata.py index 85e88bcace9..51683d6a052 100644 --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -754,7 +754,7 @@ class JobExternalOutputMetadataWrapper( object ): if dataset_path.real_path == metadata_files.dataset.file_name: return dataset_path.false_path or dataset_path.real_path return "" - line = "%s,%s,%s,%s,%s,%s" % ( + line = '"%s,%s,%s,%s,%s,%s"' % ( metadata_path_on_compute(metadata_files.filename_in), metadata_path_on_compute(metadata_files.filename_kwds), metadata_path_on_compute(metadata_files.filename_out), @@ -826,16 +826,16 @@ class JobExternalOutputMetadataWrapper( object ): sa_session.add( metadata_files ) sa_session.flush() metadata_files_list.append( metadata_files ) - args = "%s %s %s %s" % ( datatypes_config, - job_metadata, - " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ), - max_metadata_value_size) + args = '"%s" "%s" %s %s' % ( datatypes_config, + job_metadata, + " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ), + max_metadata_value_size) if include_command: # return command required to build fd, fp = tempfile.mkstemp( suffix='.py', dir=tmp_dir, prefix="set_metadata_" ) metadata_script_file = abspath( fp ) os.fdopen( fd, 'w' ).write( 'from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()' ) - return "python %s %s" % ( metadata_path_on_compute(metadata_script_file), args ) + return 'python "%s" %s' % ( metadata_path_on_compute(metadata_script_file), args ) else: # return args to galaxy_ext.metadata.set_metadata required to build return args diff --git a/lib/galaxy/datatypes/registry.py b/lib/galaxy/datatypes/registry.py index 9a8ddd75ab2..884a60b9546 100644 --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -652,11 +652,13 @@ class Registry( object ): samtools - python $set_metadata $__SET_EXTERNAL_METADATA_COMMAND_LINE__ + python "${set_metadata}" ${__SET_EXTERNAL_METADATA_COMMAND_LINE__} - + + + from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() diff --git a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py index 59272b921e3..158cdb2d260 100644 --- a/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py +++ b/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py @@ -60,13 +60,17 @@ class CloudController(BaseUIController): """ Get EC2 Account Info """ - account_info = {} - cml = cloudman.launch.CloudManLauncher(key_id, secret) - ec2_conn = cml.connect_ec2(key_id, secret) - kps = ec2_conn.get_all_key_pairs() - account_info['clusters'] = cml.get_clusters_pd() - account_info['keypairs'] = [akp.name for akp in kps] - return dumps(account_info) + try: + account_info = {} + cml = cloudman.launch.CloudManLauncher(key_id, secret) + ec2_conn = cml.connect_ec2(key_id, secret) + kps = ec2_conn.get_all_key_pairs() + account_info['clusters'] = cml.get_clusters_pd() + account_info['keypairs'] = [akp.name for akp in kps] + return dumps(account_info) + except EC2ResponseError as e: + trans.response.status = 400 + return e.message @web.expose def launch_instance(self, trans, cluster_name, password, key_id, secret, diff --git a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map index 710d4449038..74d9373c8eb 100644 --- a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map +++ b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/static/scripts/mvc/collection/list-of-pairs-collection-creator.js b/static/scripts/mvc/collection/list-of-pairs-collection-creator.js index 5ed501e2a84..ebd395c3013 100644 --- a/static/scripts/mvc/collection/list-of-pairs-collection-creator.js +++ b/static/scripts/mvc/collection/list-of-pairs-collection-creator.js @@ -1,2 +1,2 @@ -define(["utils/levenshtein","utils/natural-sort","mvc/collection/list-collection-creator","mvc/base-mvc","utils/localization","ui/hoverhighlight"],function(a,b,c,d,e){function f(a){function b(){return c.length||(c=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),c}a=a||{},a.createPair=a.createPair||function(a){return this.debug("creating pair:",a.listA[a.indexA].name,a.listB[a.indexB].name),a=a||{},this._pair(a.listA.splice(a.indexA,1)[0],a.listB.splice(a.indexB,1)[0],{silent:!0})};var c=[];return a.preprocessMatch=a.preprocessMatch||function(a){var c=b.call(this);return 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            • Entering regular expressions to match dataset names. See: ",'MDN\'s JavaScript Regular Expression Tutorial. ',"Note: forward slashes (\\) are not needed.","
              • ","
            • Clearing the filters by clicking the ",'"Clear filters" link.',"
              • ","
            "].join("")),"

            ","

            ",e(["To unpair individual dataset pairs, click the ",'unpair buttons ( ). ','Click the "Unpair all" link to unpair all pairs.'].join("")),"

            ","

            ",e(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','"Remove file extensions from pair names?" control.'].join("")),"

            ","

            ",e(['Once your collection is complete, enter a name and ','click "Create list". ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"

            "].join(""))};var j=function(a,b){var c,d=jQuery.Deferred();if(b=_.defaults(b||{},{datasets:a,oncancel:function(){Galaxy.modal.hide(),d.reject("cancelled")},oncreate:function(a,b){Galaxy.modal.hide(),d.resolve(b)}}),!window.Galaxy||!Galaxy.modal)throw new Error("Galaxy or Galaxy.modal not found");return c=new i(b),Galaxy.modal.show({title:"Create a collection of paired datasets",body:c.$el,width:"80%",height:"800px",closing_events:!0}),c.render(),window.creator=c,d};return{PairedCollectionCreator:i,pairedCollectionCreatorModal:j,createListOfPairsCollection:g}}); +define(["utils/levenshtein","utils/natural-sort","mvc/collection/list-collection-creator","mvc/base-mvc","utils/localization","ui/hoverhighlight"],function(a,b,c,d,e){function f(a){function b(){return c.length||(c=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),c}a=a||{},a.createPair=a.createPair||function(a){return this.debug("creating pair:",a.listA[a.indexA].name,a.listB[a.indexB].name),a=a||{},this._pair(a.listA.splice(a.indexA,1)[0],a.listB.splice(a.indexB,1)[0],{silent:!0})};var c=[];return a.preprocessMatch=a.preprocessMatch||function(a){var c=b.call(this);return _.extend(a,{matchTo:a.matchTo.name.replace(c[0],""),possible:a.possible.name.replace(c[1],"")})},function(b){this.debug("autopair _strategy ---------------------------"),b=b||{};var c,d=b.listA,e=b.listB,f=0,g={score:0,index:null},h=[];for(this.debug("starting list lens:",d.length,e.length),this.debug("bestMatch (starting):",JSON.stringify(g,null," "));f=k?(this.debug("creating pair"),h.push(a.createPair.call(this,{listA:d,indexA:f,listB:e,indexB:g.index})),this.debug("list lens now:",d.length,e.length)):f+=1,!d.length||!e.length)return h}return this.debug("paired:",JSON.stringify(h,null," ")),this.debug("autopair _strategy ---------------------------"),h}}function g(a){var b=a.toJSON();return j(b,{historyId:a.historyId})}var h=Backbone.View.extend(d.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(a){this.pair=a.pair||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){return this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container"),this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(a){a.currentTarget.style.opacity="0.4",a.originalEvent&&(a=a.originalEvent),a.dataTransfer.effectAllowed="move",a.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(a){a.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(a){this.$el.parent().trigger(a)},toString:function(){return"PairView("+this.pair.name+")"}}),i=Backbone.View.extend(d.LoggableMixin).extend({className:"list-of-pairs-collection-creator collection-creator flex-row-container",initialize:function(a){this.metric("PairedCollectionCreator.initialize",a),a=_.defaults(a,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=a.datasets,this.historyId=a.historyId,this.filters=this.commonFilters[a.filters]||this.commonFilters[this.DEFAULT_FILTERS],_.isArray(a.filters)&&(this.filters=a.filters),this.automaticallyPair=a.automaticallyPair,this.strategy=this.strategies[a.strategy]||this.strategies[this.DEFAULT_STRATEGY],_.isFunction(a.strategy)&&(this.strategy=a.strategy),this.matchPercentage=a.matchPercentage,this.twoPassAutopairing=a.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=a.oncancel,this.oncreate=a.oncreate,this.autoscrollDist=a.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(a){return a.sort(function(a,c){return b(a.name,c.name)}),a},_ensureIds:function(){return this.initialList.forEach(function(a){a.hasOwnProperty("id")||(a.id=_.uniqueId())}),this.initialList},_splitByFilters:function(){function a(a,b){return b.test(a.name)}var b=this.filters.map(function(a){return new RegExp(a)}),c=[[],[]];return this.unpaired.forEach(function(d){b.forEach(function(b,e){a(d,b)&&c[e].push(d)})}),c},_addToUnpaired:function(a){var c=function(d,e){if(d===e)return d;var f=Math.floor((e-d)/2)+d,g=b(a.name,this.unpaired[f].name);if(0>g)return c(d,f);if(g>0)return c(f+1,e);for(;this.unpaired[f]&&this.unpaired[f].name===a.name;)f++;return f}.bind(this);this.unpaired.splice(c(0,this.unpaired.length),0,a)},autoPair:function(a){var b=this._splitByFilters(),c=[];return this.twoPassAutopairing&&(c=this.autopairSimple({listA:b[0],listB:b[1]}),b=this._splitByFilters()),a=a||this.strategy,b=this._splitByFilters(),c=c.concat(this[a].call(this,{listA:b[0],listB:b[1]}))},autopairSimple:f({scoreThreshold:function(){return 1},match:function(a){return a=a||{},a.matchTo===a.possible?{index:a.index,score:1}:a.bestMatch}}),autopairLevenshtein:f({scoreThreshold:function(){return this.matchPercentage},match:function(b){b=b||{};var c=a(b.matchTo,b.possible),d=1-c/Math.max(b.matchTo.length,b.possible.length);return d>b.bestMatch.score?{index:b.index,score:d}:b.bestMatch}}),autopairLCS:f({scoreThreshold:function(){return this.matchPercentage},match:function(a){a=a||{};var b=this._naiveStartingAndEndingLCS(a.matchTo,a.possible).length,c=b/Math.max(a.matchTo.length,a.possible.length);return c>a.bestMatch.score?{index:a.index,score:c}:a.bestMatch}}),_naiveStartingAndEndingLCS:function(a,b){for(var c="",d="",e=0,f=0;e=0&&f>=0&&a[e]===b[f];)d=[a[e],d].join(""),e-=1,f-=1;return c+d},_pair:function(a,b,c){c=c||{};var d=this._createPair(a,b,c.name);return this.paired.push(d),this.unpaired=_.without(this.unpaired,a,b),c.silent||this.trigger("pair:new",d),d},_createPair:function(a,b,c){if(!a||!b||a===b)throw new Error("Bad pairing: "+[JSON.stringify(a),JSON.stringify(b)]);return c=c||this._guessNameForPair(a,b),{forward:a,name:c,reverse:b}},_guessNameForPair:function(a,b,c){c=void 0!==c?c:this.removeExtensions;var d=a.name,e=b.name,f=this._naiveStartingAndEndingLCS(d.replace(this.filters[0],""),e.replace(this.filters[1],""));if(c){var g=f.lastIndexOf(".");if(g>0){var h=f.slice(g,f.length);f=f.replace(h,""),d=d.replace(h,""),e=e.replace(h,"")}}return f||d+" & "+e},_unpair:function(a,b){if(b=b||{},!a)throw new Error("Bad pair: "+JSON.stringify(a));return this.paired=_.without(this.paired,a),this._addToUnpaired(a.forward),this._addToUnpaired(a.reverse),b.silent||this.trigger("pair:unpair",[a]),a},unpairAll:function(){for(var a=[];this.paired.length;)a.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",a)},_pairToJSON:function(a,b){return b=b||"hda",{collection_type:"paired",src:"new_collection",name:a.name,element_identifiers:[{name:"forward",id:a.forward.id,src:b},{name:"reverse",id:a.reverse.id,src:b}]}},createList:function(a){var b=this,c=window.Galaxy&&Galaxy.options.root?Galaxy.options.root:"/",d=c+"api/histories/"+this.historyId+"/contents/dataset_collections",e={type:"dataset_collection",collection_type:"list:paired",name:_.escape(a||b.$(".collection-name").val()),element_identifiers:b.paired.map(function(a){return b._pairToJSON(a)})};return b.blocking=!0,jQuery.ajax(d,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(e)}).always(function(){b.blocking=!1}).fail(function(a,c,d){b._ajaxErrHandler(a,c,d)}).done(function(a,c,d){b.trigger("collection:created",a,c,d),b.metric("collection:created",a),"function"==typeof b.oncreate&&b.oncreate.call(this,a,c,d)})},_ajaxErrHandler:function(a,b,c){this.error(a,b,c);var d=e("An error occurred while creating this collection");a&&(d+=0===a.readyState&&0===a.status?": "+e("Galaxy could not be reached and may be updating.")+e(" Try again in a few minutes."):a.responseJSON?"
            "+JSON.stringify(a.responseJSON)+"
            ":": "+c),creator._showAlert(d,"alert-danger")},render:function(a){return this.$el.empty().html(i.templates.main()),this._renderHeader(a),this._renderMiddle(a),this._renderFooter(a),this._addPluginComponents(),this.trigger("rendered",this),this},_renderHeader:function(){var a=this.$(".header").empty().html(i.templates.header()).find(".help-content").prepend($(i.templates.helpContent()));return this._renderFilters(),a},_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(){var a=this.$(".middle").empty().html(i.templates.middle());return this.unpairedPanelHidden?this.$(".unpaired-columns").hide():this.pairedPanelHidden&&this.$(".paired-columns").hide(),this._renderUnpaired(),this._renderPaired(),a},_renderUnpaired:function(){var a,b,c=this,d=[],f=this._splitByFilters();return this.$(".forward-column .title").text([f[0].length,e("unpaired forward")].join(" ")),this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-f[0].length)),this.$(".reverse-column .title").text([f[1].length,e("unpaired reverse")].join(" ")),this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-f[1].length)),this.$(".unpaired-columns .column-datasets").empty(),this.$(".autopair-link").toggle(0!==this.unpaired.length),0===this.unpaired.length?void this._renderUnpairedEmpty():(b=f[1].map(function(a,b){return void 0!==f[0][b]&&f[0][b]!==a&&d.push(c._renderPairButton()),c._renderUnpairedDataset(a)}),a=f[0].map(function(a){return c._renderUnpairedDataset(a)}),a.length||b.length?(this.$(".unpaired-columns .forward-column .column-datasets").append(a).add(this.$(".unpaired-columns .paired-column .column-datasets").append(d)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(b)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(a){return["(",a," ",e("filtered out"),")"].join("")},_renderUnpairedDataset:function(a){return $("
          1. ").attr("id","dataset-"+a.id).addClass("dataset unpaired").attr("draggable",!0).addClass(a.selected?"selected":"").append($("").addClass("dataset-name").text(a.name)).data("dataset",a)},_renderPairButton:function(){return $("
          2. ").addClass("dataset unpaired").append($("").addClass("dataset-name").text(e("Pair these datasets")))},_renderUnpairedEmpty:function(){var a=$('
            ').text("("+e("no remaining unpaired datasets")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(a),a},_renderUnpairedNotShown:function(){var a=$('
            ').text("("+e("no datasets were found matching the current filters")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(a),a},_adjUnpairedOnScrollbar:function(){var a=this.$(".unpaired-columns").last(),b=this.$(".unpaired-columns .reverse-column .dataset").first();if(b.size()){var c=a.offset().left+a.outerWidth(),d=b.offset().left+b.outerWidth(),e=Math.floor(c)-Math.floor(d);this.$(".unpaired-columns .forward-column").css("margin-left",e>0?e:0)}},_renderPaired:function(){if(this.$(".paired-column-title .title").text([this.paired.length,e("paired")].join(" ")),this.$(".unpair-all-link").toggle(0!==this.paired.length),0===this.paired.length)return void this._renderPairedEmpty();this.$(".remove-extensions-link").show(),this.$(".paired-columns .column-datasets").empty();var a=this;this.paired.forEach(function(b){var c=new h({pair:b});a.$(".paired-columns .column-datasets").append(c.render().$el).append(['"].join(""))})},_renderPairedEmpty:function(){var a=$('
            ').text("("+e("no paired datasets yet")+")");return this.$(".paired-columns .column-datasets").empty().prepend(a),a},_renderFooter:function(){var a=this.$(".footer").empty().html(i.templates.footer());return this.$(".remove-extensions").prop("checked",this.removeExtensions),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),a},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link"),this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(a){function b(a,b){return['"].join("")}var c=$(_.template(['
            ','
            ',e("Choose from the following filters to change which unpaired reads are shown in the display"),":
            ",_.values(this.commonFilters).map(function(a){return b(a[0],a[1])}).join(""),"
            "].join(""))({}));return this.$(a).popover({container:".collection-creator",placement:"bottom",html:!0,content:c})},_validationWarning:function(a,b){var c="validation-warning";"name"===a&&(a=this.$(".collection-name").add(this.$(".collection-name-prompt")),this.$(".collection-name").focus().select()),b?(a=a||this.$("."+c),a.removeClass(c)):a.addClass(c)},_setUpBehaviors:function(){return this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("pair:new",function(){this._renderUnpaired(),this._renderPaired(),this.$(".paired-columns").scrollTop(8e6)}),this.on("pair:unpair",function(){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.metric("filter-change",this.filters),this._renderFilters(),this._renderUnpaired()}),this.on("autopair",function(){this._renderUnpaired(),this._renderPaired();var 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.alert").hide()},_clickShowOnlyUnpaired:function(){this.$(".paired-columns").is(":visible")?this.hidePaired():this.splitView()},_clickShowOnlyPaired:function(){this.$(".unpaired-columns").is(":visible")?this.hideUnpaired():this.splitView()},hideUnpaired:function(a,b){this.unpairedPanelHidden=!0,this.pairedPanelHidden=!1,this._renderMiddle(a,b)},hidePaired:function(a,b){this.unpairedPanelHidden=!1,this.pairedPanelHidden=!0,this._renderMiddle(a,b)},splitView:function(a,b){return this.unpairedPanelHidden=this.pairedPanelHidden=!1,this._renderMiddle(a,b),this},_clickUnpairAll:function(){this.metric("unpairAll"),this.unpairAll()},_clickAutopair:function(){var a=this.autoPair();this.metric("autopair",a.length,this.unpaired.length),this.trigger("autopair")},_clickFilterChoice:function(a){var b=$(a.currentTarget);this.$(".forward-unpaired-filter input").val(b.data("forward")),this.$(".reverse-unpaired-filter input").val(b.data("reverse")),this._hideChooseFilters(),this.trigger("filter-change")},_hideChooseFilters:function(){this.$(".choose-filters-link").popover("hide"),this.$(".popover").css("display","none")},_clearFilters:function(){this.$(".forward-unpaired-filter input").val(""),this.$(".reverse-unpaired-filter input").val(""),this.trigger("filter-change")},_clickUnpairedDataset:function(a){return a.stopPropagation(),this.toggleSelectUnpaired($(a.currentTarget))},toggleSelectUnpaired:function(a,b){b=b||{};var c=a.data("dataset"),d=void 0!==b.force?b.force:!a.hasClass("selected");return a.size()&&void 0!==c?(d?(a.addClass("selected"),b.waitToPair||this.pairAllSelected()):a.removeClass("selected"),a):a},pairAllSelected:function(a){a=a||{};var b=this,c=[],d=[],e=[];return b.$(".unpaired-columns .forward-column .dataset.selected").each(function(){c.push($(this).data("dataset"))}),b.$(".unpaired-columns .reverse-column .dataset.selected").each(function(){d.push($(this).data("dataset"))}),c.length=d.length=Math.min(c.length,d.length),c.forEach(function(a,c){try{e.push(b._pair(a,d[c],{silent:!0}))}catch(f){b.error(f)}}),e.length&&!a.silent&&this.trigger("pair:new",e),e},clearSelectedUnpaired:function(){this.$(".unpaired-columns .dataset.selected").removeClass("selected")},_mousedownUnpaired:function(a){if(a.shiftKey){var b=this,c=$(a.target).addClass("selected"),d=function(a){b.$(a.target).filter(".dataset").addClass("selected")};c.parent().on("mousemove",d),$(document).one("mouseup",function(){c.parent().off("mousemove",d),b.pairAllSelected()})}},_clickPairRow:function(a){var b=$(a.currentTarget).index(),c=$(".unpaired-columns .forward-column .dataset").eq(b).data("dataset"),d=$(".unpaired-columns .reverse-column .dataset").eq(b).data("dataset");this._pair(c,d)},_startPartitionDrag:function(a){function b(){d.$(".flexible-partition-drag").css("color",""),$("body").css("cursor","").unbind("mousemove",c)}function c(a){var b=a.pageY-e;d.adjPartition(b)||$("body").trigger("mouseup"),d._adjUnpairedOnScrollbar(),e+=b}var d=this,e=a.pageY;$("body").css("cursor","ns-resize"),d.$(".flexible-partition-drag").css("color","black"),$("body").mousemove(c),$("body").one("mouseup",b)},adjPartition:function(a){var b=this.$(".unpaired-columns"),c=this.$(".paired-columns"),d=parseInt(b.css("height"),10),e=parseInt(c.css("height"),10);d=Math.max(10,d+a),e-=a;var f=0>a;if(f){if(this.unpairedPanelHidden)return!1;if(10>=d)return this.hideUnpaired(),!1}else this.unpairedPanelHidden&&(b.show(),this.unpairedPanelHidden=!1);if(f)this.pairedPanelHidden&&(c.show(),this.pairedPanelHidden=!1);else{if(this.pairedPanelHidden)return!1;if(15>=e)return this.hidePaired(),!1}return b.css({height:d+"px",flex:"0 0 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            ','',e("Unpaired forward"),"",'',"
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            ','',"
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            ','
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            ','',"
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            ','
            ','
              ',"
              ",'
              ','
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                  ','
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                    ",e(["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("")),"

                    ","

                    ",e(['Unpaired datasets are shown in the unpaired section ',"(hover over the underlined words to highlight below). ",'Paired datasets are shown in the paired section.',"

                      To pair datasets, you can:","
                    • Click a dataset in the ",'forward column ',"to select it then click a dataset in the ",'reverse column.',"
                      • ",'
                    • Click one of the "Pair these datasets" buttons in the ','middle column ',"to pair the datasets in a particular row.","
                      • ",'
                    • Click "Auto-pair" ',"to have your datasets automatically paired based on name.","
                      • ","
                    "].join("")),"

                    ","

                    ",e(["

                      You can filter what is shown in the unpaired sections by:","
                    • Entering partial dataset names in either the ",'forward filter or ','reverse filter.',"
                      • ","
                    • Choosing from a list of preset filters by clicking the ",'"Choose filters" link.',"
                      • ","
                    • Entering regular expressions to match dataset names. See: ",'MDN\'s JavaScript Regular Expression Tutorial. ',"Note: forward slashes (\\) are not needed.","
                      • ","
                    • Clearing the filters by clicking the ",'"Clear filters" link.',"
                      • ","
                    "].join("")),"

                    ","

                    ",e(["To unpair individual dataset pairs, click the ",'unpair buttons ( ). ','Click the "Unpair all" link to unpair all pairs.'].join("")),"

                    ","

                    ",e(['You can include or remove the file extensions (e.g. ".fastq") from your pair names by toggling the ','"Remove file extensions from pair names?" control.'].join("")),"

                    ","

                    ",e(['Once your collection is complete, enter a name and ','click "Create list". ',"(Note: you do not have to pair all unpaired datasets to finish.)"].join("")),"

                    "].join(""))};var j=function(a,b){var c,d=jQuery.Deferred();if(b=_.defaults(b||{},{datasets:a,oncancel:function(){Galaxy.modal.hide(),d.reject("cancelled")},oncreate:function(a,b){Galaxy.modal.hide(),d.resolve(b)}}),!window.Galaxy||!Galaxy.modal)throw new Error("Galaxy or Galaxy.modal not found");return c=new i(b),Galaxy.modal.show({title:"Create a collection of paired datasets",body:c.$el,width:"80%",height:"800px",closing_events:!0}),c.render(),window.creator=c,d};return{PairedCollectionCreator:i,pairedCollectionCreatorModal:j,createListOfPairsCollection:g}}); //# sourceMappingURL=../../../maps/mvc/collection/list-of-pairs-collection-creator.js.map \ No newline at end of file