From 9be081b6497bf9c7af5b7dcaf319b8a1ffb36a8b Mon Sep 17 00:00:00 2001 From: Nicola Soranzo Date: Tue, 3 Feb 2015 11:51:07 +0000 Subject: [PATCH 1/6] Don't abort restart if stop_daemon() failed. --- lib/galaxy/util/pastescript/serve.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/lib/galaxy/util/pastescript/serve.py b/lib/galaxy/util/pastescript/serve.py index c8006713c3c..21b809f79e2 100644 --- a/lib/galaxy/util/pastescript/serve.py +++ b/lib/galaxy/util/pastescript/serve.py @@ -559,11 +559,7 @@ class ServeCommand(Command): if cmd == 'restart' or cmd == 'stop': result = self.stop_daemon() if result: - if cmd == 'restart': - print "Could not stop daemon; aborting" - else: - print "Could not stop daemon" - return result + print "Could not stop daemon" if cmd == 'stop': return result self.options.daemon = True From 944905898b688e9a6fde4dc70031bbdc803141ae Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 10 Feb 2015 09:50:13 -0500 Subject: [PATCH 2/6] Add major version to Galaxy, expose via API. I suspect there are better ways to do this - but I thought I would put something out there we can argue about and hopefully get something in before the next release. --- lib/galaxy/config.py | 3 ++- lib/galaxy/version.py | 1 + lib/galaxy/webapps/galaxy/api/configuration.py | 5 +++++ lib/galaxy/webapps/galaxy/buildapp.py | 3 +++ 4 files changed, 11 insertions(+), 1 deletion(-) create mode 100644 lib/galaxy/version.py diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 54591391c53..9103f0cc927 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -19,7 +19,7 @@ from galaxy.util import listify from galaxy.util import string_as_bool from galaxy.util.dbkeys import GenomeBuilds from galaxy.web.formatting import expand_pretty_datetime_format - +from .version import VERSION_MAJOR log = logging.getLogger( __name__ ) @@ -63,6 +63,7 @@ class Configuration( object ): # This is not a uwsgi process, or something went horribly wrong. pass + self.version_major = VERSION_MAJOR # Database related configuration self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py new file mode 100644 index 00000000000..373d9d5c4fd --- /dev/null +++ b/lib/galaxy/version.py @@ -0,0 +1 @@ +VERSION_MAJOR = "2015.03" diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py index 6d1d17e5fdc..a14bc6d49af 100644 --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -31,6 +31,10 @@ class ConfigurationController( BaseAPIController ): serialization_params = self._parse_serialization_params( kwd, 'all' ) return self.get_config_dict( trans, is_admin, **serialization_params ) + @expose_api_anonymous + def version( self, trans, **kwds ): + return {"version_major": self.app.config.version_major } + def get_config_dict( self, trans, return_admin=False, view=None, keys=None, default_view='all' ): """ Return a dictionary with (a subset of) current Galaxy settings. @@ -97,6 +101,7 @@ class ConfigSerializer( base.ModelSerializer ): 'nginx_upload_path' : _defaults_to( self.url_for( controller='api', action='tools' ) ), 'ftp_upload_dir' : _defaults_to( None ), 'ftp_upload_site' : _defaults_to( None ), + 'version_major' : _defaults_to( None ), } diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py index d367c4fcd51..3605de8bfb3 100644 --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -222,6 +222,9 @@ def populate_api_routes( webapp, app ): webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) + webapp.mapper.connect( "configuration_version", + "/api/version", controller="configuration", + action="version", conditions=dict( method=[ "GET" ] ) ) webapp.mapper.resource( 'datatype', 'datatypes', path_prefix='/api', From 585068363465dbf483afda1271a1d94484983255 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 10 Feb 2015 10:04:19 -0500 Subject: [PATCH 3/6] Change version format to YY.MM. --- lib/galaxy/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index 373d9d5c4fd..392319a9342 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1 +1 @@ -VERSION_MAJOR = "2015.03" +VERSION_MAJOR = "15.03" From b3f39b8d5ac18c6a6c09bc6f9b9e6b3f62d5f3af Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Tue, 10 Feb 2015 13:38:30 -0500 Subject: [PATCH 4/6] UI, paired collection creator: move to underscore fn binding, allow name param in createList, add qunit test and data --- .../collection/paired-collection-creator.js | 13 +- .../collection/paired-collection-creator.js | 13 +- .../collection/paired-collection-creator.js | 2 +- templates/webapps/galaxy/root/index.mako | 6 + test/qunit/test-common.js | 1 - .../paired-collection-creator.data.js | 153 ++++++++++++++++++ test/qunit/tests/graph.js | 3 - .../tests/paired-collection-creator.html | 10 ++ test/qunit/tests/paired-collection-creator.js | 79 +++++++++ 9 files changed, 267 insertions(+), 13 deletions(-) create mode 100644 test/qunit/test-data/paired-collection-creator.data.js create mode 100644 test/qunit/tests/paired-collection-creator.html create mode 100644 test/qunit/tests/paired-collection-creator.js diff --git a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js index 73858c41db9..48f30ba3c64 100644 --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -236,14 +236,16 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte _splitByFilters : function( filters ){ var fwd = [], rev = []; - this.unpaired.forEach( function( unpaired ){ + + function _addToFwdOrRev( unpaired ){ if( this._filterFwdFn( unpaired ) ){ fwd.push( unpaired ); } if( this._filterRevFn( unpaired ) ){ rev.push( unpaired ); } - }.bind( this ) ); + } + this.unpaired.forEach( _.bind( _addToFwdOrRev, this ) ); return [ fwd, rev ]; }, @@ -603,7 +605,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte /** create the collection via the API * @returns {jQuery.xhr Object} the jquery ajax request */ - createList : function(){ + createList : function( name ){ var creator = this, url; if( creator.historyId ){ @@ -616,10 +618,11 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte var ajaxData = { type : 'dataset_collection', collection_type : 'list:paired', - name : _.escape( creator.$( '.collection-name' ).val() ), + name : _.escape( name || creator.$( '.collection-name' ).val() ), element_identifiers : creator.paired.map( function( pair ){ return creator._pairToJSON( pair ); }) + }; //this.debug( JSON.stringify( ajaxData ) ); return jQuery.ajax( url, { @@ -1732,6 +1735,8 @@ PairedCollectionCreator.templates = PairedCollectionCreator.templates || { //============================================================================= /** a modal version of the paired collection creator */ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){ + console.log( datasets ); + options = _.defaults( options || {}, { datasets : datasets, oncancel : function(){ Galaxy.modal.hide(); }, diff --git a/static/scripts/mvc/collection/paired-collection-creator.js b/static/scripts/mvc/collection/paired-collection-creator.js index 73858c41db9..48f30ba3c64 100644 --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -236,14 +236,16 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte _splitByFilters : function( filters ){ var fwd = [], rev = []; - this.unpaired.forEach( function( unpaired ){ + + function _addToFwdOrRev( unpaired ){ if( this._filterFwdFn( unpaired ) ){ fwd.push( unpaired ); } if( this._filterRevFn( unpaired ) ){ rev.push( unpaired ); } - }.bind( this ) ); + } + this.unpaired.forEach( _.bind( _addToFwdOrRev, this ) ); return [ fwd, rev ]; }, @@ -603,7 +605,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte /** create the collection via the API * @returns {jQuery.xhr Object} the jquery ajax request */ - createList : function(){ + createList : function( name ){ var creator = this, url; if( creator.historyId ){ @@ -616,10 +618,11 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte var ajaxData = { type : 'dataset_collection', collection_type : 'list:paired', - name : _.escape( creator.$( '.collection-name' ).val() ), + name : _.escape( name || creator.$( '.collection-name' ).val() ), element_identifiers : creator.paired.map( function( pair ){ return creator._pairToJSON( pair ); }) + }; //this.debug( JSON.stringify( ajaxData ) ); return jQuery.ajax( url, { @@ -1732,6 +1735,8 @@ PairedCollectionCreator.templates = PairedCollectionCreator.templates || { //============================================================================= /** a modal version of the paired collection creator */ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){ + console.log( datasets ); + options = _.defaults( options || {}, { datasets : datasets, oncancel : function(){ Galaxy.modal.hide(); }, diff --git a/static/scripts/packed/mvc/collection/paired-collection-creator.js b/static/scripts/packed/mvc/collection/paired-collection-creator.js index 31749738726..7f2ccde506a 100644 --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -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||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});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.autoscrollDist=h.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(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(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var o=0,m,s=this._splitByFilters(),h=s[0],r=s[1],q,u,k=false,t=[];while(o=this.matchPercentage){var m=this._pair(h.splice(p,1)[0],s.splice(t,1)[0],{silent:true});v.push(m);if(h.length<=0||s.length<=0){return v}}else{p+=1}}return v},autoPairLCSs:function(){var n=0,l,u=this._splitByFilters(),h=u[0],s=u[1],r,y,x,t,p,v=[];if(!h.length||!s.length){return v}while(np){t=l;p=x}}}var w=p/(Math.min(r.length,y.length));if(w>=this.matchPercentage){var k=this._pair(h.splice(n,1)[0],s.splice(t,1)[0],{silent:true});v.push(k);if(h.length<=0||s.length<=0){return v}}else{n+=1}}return v},_naiveStartingAndEndingLCS:function(m,k){var n="",o="",l=0,h=0;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+="
"+JSON.stringify(k.responseJSON)+"
"}else{i+=": "+j}}}creator._showAlert(i,"alert-danger")},render:function(h,i){this.$el.empty().html(e.templates.main());this._renderHeader(h);this._renderMiddle(h);this._renderFooter(h);this._addPluginComponents();this.trigger("rendered",this);return this},_renderHeader:function(i,j){var h=this.$(".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 $("
  • ").attr("id","dataset-"+h.id).addClass("dataset unpaired").attr("draggable",true).addClass(h.selected?"selected":"").append($("").addClass("dataset-name").text(h.name)).data("dataset",h)},_renderPairButton:function(){return $("
  • ").addClass("dataset unpaired").append($("").addClass("dataset-name").text(d("Pair these datasets")))},_renderUnpairedEmpty:function(){var h=$('
    ').text("("+d("no remaining unpaired datasets")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(h);return h},_renderUnpairedNotShown:function(){var h=$('
    ').text("("+d("no datasets were found matching the current filters")+")");this.$(".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().$el).append(['"].join(""))})},_renderPairedEmpty:function(){var h=$('
    ').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.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(h){function i(l,k){return['"].join("")}var j=$(_.template(['
    ','
    ',d("Choose from the following filters to change which unpaired reads are shown in the display"),":
    ",i("_1","_2"),i("_R1","_R2"),"
    "].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.$("."+j);i.removeClass(j)}else{i.addClass(j)}},_setUpBehaviors:function(){this.once("rendered",function(){this.trigger("rendered:initial",this)});this.on("pair:new",function(){this._renderUnpaired();this._renderPaired();this.$(".paired-columns").scrollTop(8000000)});this.on("pair:unpair",function(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();this.$(".collection-name").focus()}}else{h=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(h,i)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(h){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(h){$(h.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter 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            ');if(!j.size()){i.append(h)}else{j.before(h)}},_checkForAutoscroll:function(h,n){var l=2;var m=h.offset(),k=h.scrollTop(),i=n-m.top,j=(m.top+h.outerHeight())-n;if(i>=0&&i=0&&jo&&m-h",h.name)},toString:function(){return"PairedCollectionCreator"}});e.templates=e.templates||{main:_.template(['
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                    "].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){console.log(j);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 --git a/templates/webapps/galaxy/root/index.mako b/templates/webapps/galaxy/root/index.mako index d4514e7c125..21f10d14a16 100644 --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -152,6 +152,12 @@ currPanel.connectToQuotaMeter( Galaxy.quotaMeter ); currPanel.loadCurrentHistory(); Galaxy.currHistoryPanel = currPanel; + +currPanel.once( 'rendered', function(){ + currPanel.showSelectors(); + currPanel.selectAll(); + _.last( currPanel.actionsPopup.options ).func(); +}); }); }); diff --git a/test/qunit/test-common.js b/test/qunit/test-common.js index 6c83d793a3b..312826e2a10 100644 --- a/test/qunit/test-common.js +++ b/test/qunit/test-common.js @@ -72,7 +72,6 @@ require( [ "jquery", "QUnit" ], function( $, QUnit ) { }); - function bridge_phantomjs( QUnit ) { // Needed because the grunt task will attempt to inject this bridge assuming // QUnit is loaded directly - not using require.js. diff --git a/test/qunit/test-data/paired-collection-creator.data.js b/test/qunit/test-data/paired-collection-creator.data.js new file mode 100644 index 00000000000..f196b3c595e --- /dev/null +++ b/test/qunit/test-data/paired-collection-creator.data.js @@ -0,0 +1,153 @@ +define([], function(){ +// ============================================================================ +// plain 3 step job chain +var datasets1 = [ + { name: 'SET1-01_1.fastq' }, + { name: 'SET1-01_2.fastq' }, + { name: 'SET1-02_1.fastq' }, + { name: 'SET1-02_2.fastq' }, + { name: 'SET1-03_1.fastq' }, + { name: 'SET1-03_2.fastq' }, + { name: 'SET1-04_1.fastq' }, + { name: 'SET1-04_2.fastq' }, + { name: 'SET1-05_1.fastq' }, + { name: 'SET1-05_2.fastq' }, + { name: 'SET1-06_1.fastq' }, + { name: 'SET1-06_2.fastq' }, + { name: 'SET1-07_1.fastq' }, + { name: 'SET1-07_2.fastq' } +]; + +var datasets1CreateRequestJSON = { + "type": "dataset_collection", + "collection_type": "list:paired", + "name": "Heres a collection", + "element_identifiers": [ + { + "collection_type": "paired", + "src": "new_collection", + "name": "SET1-07", + "element_identifiers": [ + { + "name": "forward", + "id": "2", + "src": "hda" + }, + { + "name": "reverse", + "id": "3", + "src": "hda" + } + ] + }, + { + "collection_type": "paired", + "src": "new_collection", + "name": "SET1-06", + "element_identifiers": [ + { + "name": "forward", + "id": "4", + "src": "hda" + }, + { + "name": "reverse", + "id": "5", + "src": "hda" + } + ] + }, + { + "collection_type": "paired", + "src": "new_collection", + "name": "SET1-05", + "element_identifiers": [ + { + "name": "forward", + "id": "6", + "src": "hda" + }, + { + "name": "reverse", + "id": "7", + "src": "hda" + } + ] + }, + { + "collection_type": "paired", + "src": "new_collection", + "name": "SET1-04", + "element_identifiers": [ + { + "name": "forward", + "id": "8", + "src": "hda" + }, + { + "name": "reverse", + "id": "9", + "src": "hda" + } + ] + }, + { + "collection_type": "paired", + "src": "new_collection", + "name": "SET1-03", + "element_identifiers": [ + { + "name": "forward", + "id": "10", + "src": "hda" + }, + { + "name": "reverse", + "id": "11", + "src": "hda" + } + ] + }, + { + "collection_type": "paired", + "src": "new_collection", + "name": "SET1-02", + "element_identifiers": [ + { + "name": "forward", + "id": "12", + "src": "hda" + }, + { + "name": "reverse", + "id": "13", + "src": "hda" + } + ] + }, + { + "collection_type": "paired", + "src": "new_collection", + "name": "SET1-01", + "element_identifiers": [ + { + "name": "forward", + "id": "14", + "src": "hda" + }, + { + "name": "reverse", + "id": "15", + "src": "hda" + } + ] + } + ] +}; + +// ============================================================================ + return { + _1 : datasets1, + _1requestJSON : datasets1CreateRequestJSON + }; +}); diff --git a/test/qunit/tests/graph.js b/test/qunit/tests/graph.js index 17e16e201dd..baead23cf24 100644 --- a/test/qunit/tests/graph.js +++ b/test/qunit/tests/graph.js @@ -1,11 +1,8 @@ -// This file isn't really testing anything useful yet, it is just testing -// (or demonstrating) qunit+backbone interactions. define([ "utils/graph", "jquery", "sinon-qunit" ], function( GRAPH, $, sinon ){ - console.debug( '' ); /*globals equal ok, test module expect deepEqual strictEqual */ "use strict"; diff --git a/test/qunit/tests/paired-collection-creator.html b/test/qunit/tests/paired-collection-creator.html new file mode 100644 index 00000000000..00e97f6ea8c --- /dev/null +++ b/test/qunit/tests/paired-collection-creator.html @@ -0,0 +1,10 @@ + + + + + + + + + diff --git a/test/qunit/tests/paired-collection-creator.js b/test/qunit/tests/paired-collection-creator.js new file mode 100644 index 00000000000..df3e866f7b3 --- /dev/null +++ b/test/qunit/tests/paired-collection-creator.js @@ -0,0 +1,79 @@ +define([ + "mvc/collection/paired-collection-creator", + "test-data/paired-collection-creator.data", + "jquery", + "sinon-qunit", + "galaxy.base" +], function( + PAIRED_COLLECTION_CREATOR, + // why am I yelling? + DATA, + $, + sinon +){ + /*globals equal test module expect deepEqual strictEqual throws ok */ + "use strict"; + var PCC = PAIRED_COLLECTION_CREATOR.PairedCollectionCreator; + + module( "Galaxy client app tests" ); + + test( "Creator base/empty construction/initializiation defaults", function() { + var pcc = new PCC([]); + ok( pcc instanceof PCC ); + ok( pcc.hasOwnProperty( 'options' ) && typeof pcc.options === 'object' ); + deepEqual( pcc.options.filters, pcc.DEFAULT_FILTERS ); + ok( pcc.options.automaticallyPair ); + equal( pcc.options.matchPercentage, 1.0 ); + equal( pcc.options.strategy, 'lcs' ); + }); + + test( "Creator construction/initializiation with datasets", function() { + var pcc = new PCC({ + datasets : DATA._1 + }); + //pcc.initialList.forEach( function( dataset, i ){ + // console.log( i + ':\n' + JSON.stringify( dataset ) ); + //}); + // pcc maintains the original list - which, in this case, is already sorted + deepEqual( pcc.initialList, DATA._1 ); + // datasets 1 has no ids, so the pcc will create them + ok( _.every( pcc.initialList, function( dataset ){ + return dataset.id; + })); + // datasets 1 is very easy to auto pair + equal( pcc.unpaired.length, 0 ); + equal( pcc.paired.length, pcc.initialList.length / 2 ); + }); + + //TODO: + // filters: clearing, setting via popover, regex + // partition: maximize paired, maximize unpaired, split evenly + // pairing: manually pairing and unpairing + // misc: renaming pairs, removing file extensions + + test( "Collection creation", function() { + var pcc = new PCC({ + datasets : DATA._1, + historyId : 'fakeHistoryId' + }), + server = sinon.fakeServer.create(); + + var requestJSON; + server.respondWith( 'POST', '/api/histories/fakeHistoryId/contents/dataset_collections', function( request ){ + requestJSON = JSON.parse( request.requestBody ); + request.respond( + 200, + { "Content-Type": "application/json" }, + JSON.stringify({ + fakeResponse: 'yes' + }) + ); + }); + + console.debug( 'requestBody:', JSON.stringify( requestJSON, null, ' ' ) ); + pcc.createList( 'Heres a collection' ); + server.respond(); + deepEqual( requestJSON, DATA._1requestJSON ); + }); + +}); From 3ec57d0833aed85dcc98cfd6b451b1c555b5cafa Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Tue, 10 Feb 2015 13:42:59 -0500 Subject: [PATCH 5/6] UI, utils: modularize (AMD) naturalSort and move to utils --- client/galaxy/scripts/galaxy.base.js | 27 ----------------- .../collection/paired-collection-creator.js | 3 +- client/galaxy/scripts/utils/natural-sort.js | 30 +++++++++++++++++++ static/scripts/galaxy.base.js | 27 ----------------- .../collection/paired-collection-creator.js | 3 +- static/scripts/packed/galaxy.base.js | 2 +- .../collection/paired-collection-creator.js | 2 +- static/scripts/packed/utils/natural-sort.js | 1 + static/scripts/utils/natural-sort.js | 30 +++++++++++++++++++ test/qunit/tests/paired-collection-creator.js | 3 +- 10 files changed, 68 insertions(+), 60 deletions(-) create mode 100644 client/galaxy/scripts/utils/natural-sort.js create mode 100644 static/scripts/packed/utils/natural-sort.js create mode 100644 static/scripts/utils/natural-sort.js diff --git a/client/galaxy/scripts/galaxy.base.js b/client/galaxy/scripts/galaxy.base.js index 57e48c40c7c..771dac788ba 100644 --- a/client/galaxy/scripts/galaxy.base.js +++ b/client/galaxy/scripts/galaxy.base.js @@ -207,33 +207,6 @@ function make_popup_menus( parent ) { }); } -// Alphanumeric/natural sort fn -function naturalSort(a, b) { - // setup temp-scope variables for comparison evauluation - var re = /(-?[0-9\.]+)/g, - x = a.toString().toLowerCase() || '', - y = b.toString().toLowerCase() || '', - nC = String.fromCharCode(0), - xN = x.replace( re, nC + '$1' + nC ).split(nC), - yN = y.replace( re, nC + '$1' + nC ).split(nC), - xD = (new Date(x)).getTime(), - yD = xD ? (new Date(y)).getTime() : null; - // natural sorting of dates - if ( yD ) { - if ( xD < yD ) { return -1; } - else if ( xD > yD ) { return 1; } - } - // natural sorting through split numeric strings and default strings - var oFxNcL, oFyNcL; - for ( var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++ ) { - oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc]; - oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc]; - if (oFxNcL < oFyNcL) { return -1; } - else if (oFxNcL > oFyNcL) { return 1; } - } - return 0; -} - $.fn.refresh_select2 = function() { var select_elt = $(this); var options = { placeholder:'Click to select', diff --git a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js index 48f30ba3c64..2fea170c5d8 100644 --- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/paired-collection-creator.js @@ -1,8 +1,9 @@ define([ "utils/levenshtein", + "utils/natural-sort", "mvc/base-mvc", "utils/localization" -], function( levelshteinDistance, baseMVC, _l ){ +], function( levelshteinDistance, naturalSort, baseMVC, _l ){ /* ============================================================================ TODO: _adjPairedOnScrollBar diff --git a/client/galaxy/scripts/utils/natural-sort.js b/client/galaxy/scripts/utils/natural-sort.js new file mode 100644 index 00000000000..1f6cc5cc059 --- /dev/null +++ b/client/galaxy/scripts/utils/natural-sort.js @@ -0,0 +1,30 @@ +define([], function(){ +// Alphanumeric/natural sort fn +function naturalSort(a, b) { + // setup temp-scope variables for comparison evauluation + var re = /(-?[0-9\.]+)/g, + x = a.toString().toLowerCase() || '', + y = b.toString().toLowerCase() || '', + nC = String.fromCharCode(0), + xN = x.replace( re, nC + '$1' + nC ).split(nC), + yN = y.replace( re, nC + '$1' + nC ).split(nC), + xD = (new Date(x)).getTime(), + yD = xD ? (new Date(y)).getTime() : null; + // natural sorting of dates + if ( yD ) { + if ( xD < yD ) { return -1; } + else if ( xD > yD ) { return 1; } + } + // natural sorting through split numeric strings and default strings + var oFxNcL, oFyNcL; + for ( var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++ ) { + oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc]; + oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc]; + if (oFxNcL < oFyNcL) { return -1; } + else if (oFxNcL > oFyNcL) { return 1; } + } + return 0; +} + +return naturalSort; +}) diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js index 57e48c40c7c..771dac788ba 100644 --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -207,33 +207,6 @@ function make_popup_menus( parent ) { }); } -// Alphanumeric/natural sort fn -function naturalSort(a, b) { - // setup temp-scope variables for comparison evauluation - var re = /(-?[0-9\.]+)/g, - x = a.toString().toLowerCase() || '', - y = b.toString().toLowerCase() || '', - nC = String.fromCharCode(0), - xN = x.replace( re, nC + '$1' + nC ).split(nC), - yN = y.replace( re, nC + '$1' + nC ).split(nC), - xD = (new Date(x)).getTime(), - yD = xD ? (new Date(y)).getTime() : null; - // natural sorting of dates - if ( yD ) { - if ( xD < yD ) { return -1; } - else if ( xD > yD ) { return 1; } - } - // natural sorting through split numeric strings and default strings - var oFxNcL, oFyNcL; - for ( var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++ ) { - oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc]; - oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc]; - if (oFxNcL < oFyNcL) { return -1; } - else if (oFxNcL > oFyNcL) { return 1; } - } - return 0; -} - $.fn.refresh_select2 = function() { var select_elt = $(this); var options = { placeholder:'Click to select', diff --git a/static/scripts/mvc/collection/paired-collection-creator.js b/static/scripts/mvc/collection/paired-collection-creator.js index 48f30ba3c64..2fea170c5d8 100644 --- a/static/scripts/mvc/collection/paired-collection-creator.js +++ b/static/scripts/mvc/collection/paired-collection-creator.js @@ -1,8 +1,9 @@ define([ "utils/levenshtein", + "utils/natural-sort", "mvc/base-mvc", "utils/localization" -], function( levelshteinDistance, baseMVC, _l ){ +], function( levelshteinDistance, naturalSort, baseMVC, _l ){ /* ============================================================================ TODO: _adjPairedOnScrollBar diff --git a/static/scripts/packed/galaxy.base.js b/static/scripts/packed/galaxy.base.js index 4d6becdd534..4d86c1913f0 100644 --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1 +1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a");var f=b.data("menu_options");if(obj_length(f)<=0){$("
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                    ").append(g).appendTo("body");var e=d.pageX-h.width()/2;e=Math.min(e,$(document).scrollLeft()+$(window).width()-$(h).width()-5);e=Math.max(e,$(document).scrollLeft()+5);h.css({top:d.pageY,left:e})},10);setTimeout(function(){var f=function(h){$(h).bind("click.close_popup",function(){$(".popmenu-wrapper").remove();h.unbind("click.close_popup")})};f($(window.document));f($(window.top.document));for(var e=window.top.frames.length;e--;){var g=$(window.top.frames[e].document);f(g)}},50);return false})}function make_popup_menus(a){a=a||document;$(a).find("div[popupmenu]").each(function(){var b={};var d=$(this);d.find("a").each(function(){var g=$(this),i=g.get(0),e=i.getAttribute("confirm"),f=i.getAttribute("href"),h=i.getAttribute("target");if(!f){b[g.text()]=null}else{b[g.text()]={url:f,action:function(){if(!e||confirm(e)){if(h){window.open(f,h);return false}else{g.click()}}}}}});var c=$(a).find("#"+d.attr("popupmenu"));c.find("a").bind("click",function(f){f.stopPropagation();return true});make_popupmenu(c,b);c.addClass("popup");d.remove()})}function naturalSort(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(do){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);if){return 1}}}return 0}$.fn.refresh_select2=function(){var b=$(this);var a={placeholder:"Click to select",closeOnSelect:!b.is("[MULTIPLE]"),dropdownAutoWidth:true,containerCssClass:"select2-minwidth"};return b.select2(a)};function replace_big_select_inputs(a,c,b){if(!jQuery.fn.select2){return}if(a===undefined){a=20}if(c===undefined){c=3000}b=b||$("select");b.each(function(){var e=$(this).not("[multiple]");var d=e.find("option").length;if((dc)){return}if(e.hasClass("no-autocomplete")){return}e.refresh_select2()})}$.fn.make_text_editable=function(g){var d=("num_cols" in g?g.num_cols:30),c=("num_rows" in g?g.num_rows:4),e=("use_textarea" in g?g.use_textarea:false),b=("on_finish" in g?g.on_finish:null),f=("help_text" in g?g.help_text:null);var a=$(this);a.addClass("editable-text").click(function(l){if($(this).children(":input").length>0){return}a.removeClass("editable-text");var i=function(m){a.find(":input").remove();if(m!==""){a.text(m)}else{a.html("
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c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return 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b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}jQuery.fn.preventDoubleSubmission=function(){$(this).on("submit",function(b){var a=$(this);if(a.data("submitted")===true){b.preventDefault()}else{a.data("submitted",true)}});return this};$(document).ready(function(){init_refresh_on_change();if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip()}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/collection/paired-collection-creator.js b/static/scripts/packed/mvc/collection/paired-collection-creator.js index 7f2ccde506a..bb7a1a8f61d 100644 --- a/static/scripts/packed/mvc/collection/paired-collection-creator.js +++ b/static/scripts/packed/mvc/collection/paired-collection-creator.js @@ -1 +1 @@ -define(["utils/levenshtein","mvc/base-mvc","utils/localization"],function(g,a,d){var f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(h){this.pair=h.pair||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(h){h.currentTarget.style.opacity="0.4";if(h.originalEvent){h=h.originalEvent}h.dataTransfer.effectAllowed="move";h.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(h){h.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(h){this.$el.parent().trigger(h)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(h){h=_.defaults(h,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=h.datasets;this.historyId=h.historyId;this.filters=this.commonFilters[h.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(h.filters)){this.filters=h.filters}this.automaticallyPair=h.automaticallyPair;this.matchPercentage=h.matchPercentage;this.strategy=this.strategies[h.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(h.strategy)){this.strategy=h.strategy}this.removeExtensions=true;this.oncancel=h.oncancel;this.oncreate=h.oncreate;this.autoscrollDist=h.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(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(k){var j=[],h=[];function i(l){if(this._filterFwdFn(l)){j.push(l)}if(this._filterRevFn(l)){h.push(l)}}this.unpaired.forEach(_.bind(i,this));return[j,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(i){i=i||this.strategy;var h=this.simpleAutoPair();h=h.concat(this[i].call(this));return h},simpleAutoPair:function(){var 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"+[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(j){var 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                            ",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("")),"

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                              You can filter what is shown in the unpaired sections by:","
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f=Backbone.View.extend(a.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(i){this.pair=i.pair||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){this.$el.attr("draggable",true).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container");return this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(i){i.currentTarget.style.opacity="0.4";if(i.originalEvent){i=i.originalEvent}i.dataTransfer.effectAllowed="move";i.dataTransfer.setData("text/plain",JSON.stringify(this.pair));this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(i){i.currentTarget.style.opacity="1.0";this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(i){this.$el.parent().trigger(i)},toString:function(){return"PairView("+this.pair.name+")"}});var e=Backbone.View.extend(a.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(i){i=_.defaults(i,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:true,matchPercentage:1,strategy:"lcs"});this.initialList=i.datasets;this.historyId=i.historyId;this.filters=this.commonFilters[i.filters]||this.commonFilters[this.DEFAULT_FILTERS];if(_.isArray(i.filters)){this.filters=i.filters}this.automaticallyPair=i.automaticallyPair;this.matchPercentage=i.matchPercentage;this.strategy=this.strategies[i.strategy]||this.strategies[this.DEFAULT_STRATEGY];if(_.isFunction(i.strategy)){this.strategy=i.strategy}this.removeExtensions=true;this.oncancel=i.oncancel;this.oncreate=i.oncreate;this.autoscrollDist=i.autoscrollDist||24;this.unpairedPanelHidden=false;this.pairedPanelHidden=false;this.$dragging=null;this._setUpBehaviors();this._dataSetUp()},commonFilters:{none:["",""],illumina:["_1","_2"]},DEFAULT_FILTERS:"illumina",strategies:{lcs:"autoPairLCSs",levenshtein:"autoPairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[];this.unpaired=[];this.selectedIds=[];this._sortInitialList();this._ensureIds();this.unpaired=this.initialList.slice(0);if(this.automaticallyPair){this.autoPair();this.once("rendered:initial",function(){this.trigger("autopair")})}},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(i){i.sort(function(k,j){return g(k.name,j.name)});return i},_ensureIds:function(){this.initialList.forEach(function(i){if(!i.hasOwnProperty("id")){i.id=_.uniqueId()}});return this.initialList},_splitByFilters:function(l){var k=[],i=[];function j(m){if(this._filterFwdFn(m)){k.push(m)}if(this._filterRevFn(m)){i.push(m)}}this.unpaired.forEach(_.bind(j,this));return[k,i]},_filterFwdFn:function(j){var i=new RegExp(this.filters[0]);return i.test(j.name)},_filterRevFn:function(j){var i=new RegExp(this.filters[1]);return i.test(j.name)},_addToUnpaired:function(j){var i=function(k,m){if(k===m){return k}var l=Math.floor((m-k)/2)+k,n=g(j.name,this.unpaired[l].name);if(n<0){return i(k,l)}else{if(n>0){return i(l+1,m)}}while(this.unpaired[l]&&this.unpaired[l].name===j.name){l++}return l}.bind(this);this.unpaired.splice(i(0,this.unpaired.length),0,j)},autoPair:function(j){j=j||this.strategy;var i=this.simpleAutoPair();i=i.concat(this[j].call(this));return i},simpleAutoPair:function(){var p=0,n,t=this._splitByFilters(),k=t[0],s=t[1],r,v,l=false,u=[];while(p=this.matchPercentage){var n=this._pair(k.splice(q,1)[0],t.splice(u,1)[0],{silent:true});w.push(n);if(k.length<=0||t.length<=0){return w}}else{q+=1}}return w},autoPairLCSs:function(){var o=0,m,v=this._splitByFilters(),k=v[0],t=v[1],s,z,y,u,q,w=[];if(!k.length||!t.length){return w}while(oq){u=m;q=y}}}var x=q/(Math.min(s.length,z.length));if(x>=this.matchPercentage){var l=this._pair(k.splice(o,1)[0],t.splice(u,1)[0],{silent:true});w.push(l);if(k.length<=0||t.length<=0){return w}}else{o+=1}}return w},_naiveStartingAndEndingLCS:function(n,l){var o="",p="",m=0,k=0;while(m=0&&k>=0){if(n[m]!==l[k]){break}p=[n[m],p].join("");m-=1;k-=1}return o+p},_pair:function(k,i,j){j=j||{};var l=this._createPair(k,i,j.name);this.paired.push(l);this.unpaired=_.without(this.unpaired,k,i);if(!j.silent){this.trigger("pair:new",l)}return l},_createPair:function(k,i,j){if(!(k&&i)||(k===i)){throw new Error("Bad pairing: "+[JSON.stringify(k),JSON.stringify(i)])}j=j||this._guessNameForPair(k,i);return{forward:k,name:j,reverse:i}},_guessNameForPair:function(k,i,l){l=(l!==undefined)?(l):(this.removeExtensions);var j=this._naiveStartingAndEndingLCS(k.name.replace(this.filters[0],""),i.name.replace(this.filters[1],""));if(l){var m=j.lastIndexOf(".");if(m>0){j=j.slice(0,m)}}return j||(k.name+" & "+i.name)},_unpair:function(j,i){i=i||{};if(!j){throw new Error("Bad pair: "+JSON.stringify(j))}this.paired=_.without(this.paired,j);this._addToUnpaired(j.forward);this._addToUnpaired(j.reverse);if(!i.silent){this.trigger("pair:unpair",[j])}return j},unpairAll:function(){var i=[];while(this.paired.length){i.push(this._unpair(this.paired[0],{silent:true}))}this.trigger("pair:unpair",i)},_pairToJSON:function(i){return{collection_type:"paired",src:"new_collection",name:i.name,element_identifiers:[{name:"forward",id:i.forward.id,src:"hda"},{name:"reverse",id:i.reverse.id,src:"hda"}]}},createList:function(k){var l=this,j;if(l.historyId){j="/api/histories/"+this.historyId+"/contents/dataset_collections"}var i={type:"dataset_collection",collection_type:"list:paired",name:_.escape(k||l.$(".collection-name").val()),element_identifiers:l.paired.map(function(m){return l._pairToJSON(m)})};return jQuery.ajax(j,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(i)}).fail(function(o,m,n){l._ajaxErrHandler(o,m,n)}).done(function(m,n,o){l.trigger("collection:created",m,n,o);if(typeof l.oncreate==="function"){l.oncreate.call(this,m,n,o)}})},_ajaxErrHandler:function(l,i,k){this.error(l,i,k);var j=d("An error occurred while creating this collection");if(l){if(l.readyState===0&&l.status===0){j+=": "+d("Galaxy could not be reached and may be updating.")+d(" Try again in a few minutes.")}else{if(l.responseJSON){j+="
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                          1. ").attr("id","dataset-"+i.id).addClass("dataset unpaired").attr("draggable",true).addClass(i.selected?"selected":"").append($("").addClass("dataset-name").text(i.name)).data("dataset",i)},_renderPairButton:function(){return $("
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                            ').text("("+d("no datasets were found matching the current filters")+")");this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(i);return i},_adjUnpairedOnScrollbar:function(){var l=this.$(".unpaired-columns").last(),m=this.$(".unpaired-columns .reverse-column .dataset").first();if(!m.size()){return}var i=l.offset().left+l.outerWidth(),k=m.offset().left+m.outerWidth(),j=Math.floor(i)-Math.floor(k);this.$(".unpaired-columns .forward-column").css("margin-left",(j>0)?j:0)},_renderPaired:function(j,k){this.$(".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.$(".paired-columns .column-datasets").empty();var i=this;this.paired.forEach(function(n,l){var m=new f({pair:n});i.$(".paired-columns .column-datasets").append(m.render().$el).append(['"].join(""))})},_renderPairedEmpty:function(){var i=$('
                            ').text("("+d("no paired datasets yet")+")");this.$(".paired-columns .column-datasets").empty().prepend(i);return i},_renderFooter:function(j,k){var i=this.$(".footer").empty().html(e.templates.footer());this.$(".remove-extensions").prop("checked",this.removeExtensions);if(typeof this.oncancel==="function"){this.$(".cancel-create.btn").show()}return i},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link");this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(i){function j(m,l){return['"].join("")}var k=$(_.template(['
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i,j=null;if(this.paired.length){j="alert-success";i=this.paired.length+" "+d("pairs created");if(!this.unpaired.length){i+=": "+d("all datasets have been successfully paired");this.hideUnpaired();this.$(".collection-name").focus()}}else{i=d("Could not automatically create any pairs from the given dataset names")}this._showAlert(i,j)});return this},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .header .alert button":"_hideAlert","click .forward-column .column-title":"_clickShowOnlyUnpaired","click .reverse-column .column-title":"_clickShowOnlyUnpaired","click .unpair-all-link":"_clickUnpairAll","change .forward-unpaired-filter input":function(i){this.trigger("filter-change")},"focus .forward-unpaired-filter input":function(i){$(i.currentTarget).select()},"click .autopair-link":"_clickAutopair","click .choose-filters .filter-choice":"_clickFilterChoice","click .clear-filters-link":"_clearFilters","change .reverse-unpaired-filter 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                                    ",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("")),"

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                                    ",d(['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:","
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                                      • ",'
                                    • Click one of the "Pair these datasets" buttons in the ','middle column ',"to pair the datasets in a particular row.","
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                                      You can filter what is shown in the unpaired sections by:","
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                                      • ","
                                    • 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.","
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                                    ","

                                    ",d(['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(""))};(function(){jQuery.fn.extend({hoverhighlight:function i(k,j){k=k||"body";if(!this.size()){return this}$(this).each(function(){var m=$(this),l=m.data("target");if(l){m.mouseover(function(n){$(l,k).css({background:j})}).mouseout(function(n){$(l).css({background:""})})}});return this}})}());var b=function c(k,i){console.log(k);i=_.defaults(i||{},{datasets:k,oncancel:function(){Galaxy.modal.hide()},oncreate:function(){Galaxy.modal.hide();Galaxy.currHistoryPanel.refreshContents()}});if(!window.Galaxy||!Galaxy.modal){throw new Error("Galaxy or Galaxy.modal not found")}var j=new e(i).render();Galaxy.modal.show({title:"Create a collection of paired datasets",body:j.$el,width:"80%",height:"800px",closing_events:true});window.PCC=j;return j};return{PairedCollectionCreator:e,pairedCollectionCreatorModal:b}}); \ No newline at end of file diff --git a/static/scripts/packed/utils/natural-sort.js b/static/scripts/packed/utils/natural-sort.js new file mode 100644 index 00000000000..43be28f37d3 --- /dev/null +++ b/static/scripts/packed/utils/natural-sort.js @@ -0,0 +1 @@ +define([],function(){function a(j,h){var p=/(-?[0-9\.]+)/g,k=j.toString().toLowerCase()||"",g=h.toString().toLowerCase()||"",l=String.fromCharCode(0),n=k.replace(p,l+"$1"+l).split(l),e=g.replace(p,l+"$1"+l).split(l),d=(new Date(k)).getTime(),o=d?(new Date(g)).getTime():null;if(o){if(do){return 1}}}var m,f;for(var i=0,c=Math.max(n.length,e.length);if){return 1}}}return 0}return a}); \ No newline at end of file diff --git a/static/scripts/utils/natural-sort.js b/static/scripts/utils/natural-sort.js new file mode 100644 index 00000000000..1f6cc5cc059 --- /dev/null +++ b/static/scripts/utils/natural-sort.js @@ -0,0 +1,30 @@ +define([], function(){ +// Alphanumeric/natural sort fn +function naturalSort(a, b) { + // setup temp-scope variables for comparison evauluation + var re = /(-?[0-9\.]+)/g, + x = a.toString().toLowerCase() || '', + y = b.toString().toLowerCase() || '', + nC = String.fromCharCode(0), + xN = x.replace( re, nC + '$1' + nC ).split(nC), + yN = y.replace( re, nC + '$1' + nC ).split(nC), + xD = (new Date(x)).getTime(), + yD = xD ? (new Date(y)).getTime() : null; + // natural sorting of dates + if ( yD ) { + if ( xD < yD ) { return -1; } + else if ( xD > yD ) { return 1; } + } + // natural sorting through split numeric strings and default strings + var oFxNcL, oFyNcL; + for ( var cLoc = 0, numS = Math.max(xN.length, yN.length); cLoc < numS; cLoc++ ) { + oFxNcL = parseFloat(xN[cLoc]) || xN[cLoc]; + oFyNcL = parseFloat(yN[cLoc]) || yN[cLoc]; + if (oFxNcL < oFyNcL) { return -1; } + else if (oFxNcL > oFyNcL) { return 1; } + } + return 0; +} + +return naturalSort; +}) diff --git a/test/qunit/tests/paired-collection-creator.js b/test/qunit/tests/paired-collection-creator.js index df3e866f7b3..c3d6cd4e6ad 100644 --- a/test/qunit/tests/paired-collection-creator.js +++ b/test/qunit/tests/paired-collection-creator.js @@ -2,8 +2,7 @@ define([ "mvc/collection/paired-collection-creator", "test-data/paired-collection-creator.data", "jquery", - "sinon-qunit", - "galaxy.base" + "sinon-qunit" ], function( PAIRED_COLLECTION_CREATOR, // why am I yelling? From 863704d8503e93904cf8842d86f1e1cb19167f7b Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 10 Feb 2015 14:07:01 -0500 Subject: [PATCH 6/6] Followup to PR https://bitbucket.org/galaxy/galaxy-central/pull-request/658/, only continue restarting in the case of a 1 return code from stop_daemon --- lib/galaxy/util/pastescript/serve.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/lib/galaxy/util/pastescript/serve.py b/lib/galaxy/util/pastescript/serve.py index 21b809f79e2..4bd3a0c9b4e 100644 --- a/lib/galaxy/util/pastescript/serve.py +++ b/lib/galaxy/util/pastescript/serve.py @@ -560,6 +560,10 @@ class ServeCommand(Command): result = self.stop_daemon() if result: print "Could not stop daemon" + # It's ok to continue trying to restart if stop_daemon returns + # a 1, otherwise shortcut and return. + if cmd == 'restart' and result != 1: + return result if cmd == 'stop': return result self.options.daemon = True