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commit/galaxy-central: carlfeberhard: Fix to 264657d: make infomessage and persistent across states; Style tweaks
by commits-noreply＠bitbucket.org 13 Aug '14

13 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b2dc0bd882a/ Changeset: 9b2dc0bd882a User: carlfeberhard Date: 2014-08-13 16:03:29 Summary: Fix to 264657d: make infomessage and persistent across states; Style tweaks Affected #: 4 files diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r 9b2dc0bd882a0432809f455acce191c333b8df02 static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -4,7 +4,13 @@ "utils/localization" ], function( STATES, BASE_MVC, _l ){ /* global Backbone */ -//============================================================================== +/*============================================================================== +TODO: + straighten out state rendering and templates used + inaccessible/STATES.NOT_VIEWABLE is a special case + simplify button rendering + +==============================================================================*/ var _super = BASE_MVC.ListItemView; /** @class Read only list view for either LDDAs, HDAs, or HDADCEs. * Roughly, any DatasetInstance (and not a raw Dataset). @@ -196,9 +202,16 @@ */ _renderDetails : function(){ //TODO: generalize to be allow different details for each state + + // no access - render nothing but a message + if( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ){ + return $( this.templates.noAccess( this.model.toJSON(), this ) ); + } + var $details = _super.prototype._renderDetails.call( this ); $details.find( '.actions .left' ).empty().append( this._renderSecondaryActions() ); - $details.find( '.summary' ).html( this._renderSummary() ); + $details.find( '.summary' ).html( this._renderSummary() ) + .prepend( this._renderDetailMessages() ); $details.find( '.display-applications' ).html( this._renderDisplayApplications() ); //TODO: double tap @@ -214,6 +227,18 @@ return summaryRenderFn( json, this ); }, + /** Render messages to be displayed only when the details are shown */ + _renderDetailMessages : function(){ + var view = this, + $warnings = $( '<div class="detail-messages"></div>' ), + json = view.model.toJSON(); +//TODO:! unordered (map) + _.each( view.templates.detailMessages, function( templateFn ){ + $warnings.append( $( templateFn( json, view ) ) ); + }); + return $warnings; + }, + /** Render the external display application links */ _renderDisplayApplications : function(){ if( this.model.isDeletedOrPurged() ){ return ''; } @@ -369,6 +394,14 @@ '</div>' ], 'dataset' ); + var noAccessTemplate = BASE_MVC.wrapTemplate([ + '<div class="details">', + '<div class="summary">', + _l( 'You do not have permission to view this dataset' ), + '</div>', + '</div>' + ], 'dataset' ); + //TODO: still toooooooooooooo complex - rework var summaryTemplates = {}; summaryTemplates[ STATES.OK ] = summaryTemplates[ STATES.FAILED_METADATA ] = BASE_MVC.wrapTemplate([ @@ -410,22 +443,10 @@ '<div>', _l( 'The job creating this dataset was cancelled before completion' ), '</div>' ], 'dataset' ); summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([ - '<div>', - '<% if( dataset.resubmitted ){ %>', - _l( 'The job creating this dataset has been resubmitted is now waiting to run' ), - '<% } else { %>', - _l( 'This job is waiting to run' ), - '<% } %>', - '</div>' + '<div>', _l( 'This job is waiting to run' ), '</div>' ], 'dataset' ); summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([ - '<div>', - '<% if( dataset.resubmitted ){ %>', - _l( 'The job creating this dataset has been resubmitted is now running' ), - '<% } else { %>', - _l( 'This job is currently running' ), - '<% } %>', - '</div>' + '<div>', _l( 'This job is currently running' ), '</div>' ], 'dataset' ); summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([ '<div>', _l( 'This dataset is currently uploading' ), '</div>' @@ -450,6 +471,18 @@ '<div>Error: unknown dataset state: "<%- dataset.state %>"</div>' ], 'dataset' ); + // messages to be displayed only within the details section ('below the fold') + var detailMessageTemplates = { + resubmitted : BASE_MVC.wrapTemplate([ + // deleted not purged + '<% if( model.resubmitted ){ %>', + '<div class="resubmitted-msg infomessagesmall">', + _l( 'The job creating this dataset has been resubmitted' ), + '</div>', + '<% } %>' + ]) + }; + // this is applied to both old and new style display apps var displayApplicationsTemplate = BASE_MVC.wrapTemplate([ '<% _.each( apps, function( app ){ %>', @@ -469,7 +502,9 @@ return _.extend( {}, _super.prototype.templates, { warnings : warnings, details : detailsTemplate, + noAccess : noAccessTemplate, summaries : summaryTemplates, + detailMessages : detailMessageTemplates, displayApplications : displayApplicationsTemplate }); }()); diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r 9b2dc0bd882a0432809f455acce191c333b8df02 static/scripts/packed/mvc/dataset/dataset-li.js --- a/static/scripts/packed/mvc/dataset/dataset-li.js +++ b/static/scripts/packed/mvc/dataset/dataset-li.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.model.toJSON(),g=this.templates.summaries[f.state];g=g||this.templates.summaries.unknown;return g(f,this)},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var g=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var h=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var i={};i[a.OK]=i[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");i[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");i[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");i[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");i[a.QUEUED]=b.wrapTemplate(["<div>","<% if( dataset.resubmitted ){ %>",c("The job creating this dataset has been resubmitted is now waiting to run"),"<% } else { %>",c("This job is waiting to run"),"<% } %>","</div>"],"dataset");i[a.RUNNING]=b.wrapTemplate(["<div>","<% if( dataset.resubmitted ){ %>",c("The job creating this dataset has been resubmitted is now running"),"<% } else { %>",c("This job is currently running"),"<% } %>","</div>"],"dataset");i[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");i[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");i[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");i[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");i[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");i.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:g,details:h,summaries:i,displayApplications:f})}());return{DatasetListItemView:d}}); \ No newline at end of file +define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.model.toJSON(),g=this.templates.summaries[f.state];g=g||this.templates.summaries.unknown;return g(f,this)},_renderDetailMessages:function(){var f=this,h=$('<div class="detail-messages"></div>'),g=f.model.toJSON();_.each(f.templates.detailMessages,function(i){h.append($(i(g,f)))});return h},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var h=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var i=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var g=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var j={};j[a.OK]=j[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");j[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");j[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");j[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");j[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");j[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");j[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");j[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");j[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");j[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");j[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");j.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var k={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:h,details:i,noAccess:g,summaries:j,detailMessages:k,displayApplications:f})}());return{DatasetListItemView:d}}); \ No newline at end of file diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r 9b2dc0bd882a0432809f455acce191c333b8df02 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1684,13 +1684,13 @@ .dataset .details .actions .left .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} .dataset .details .actions .left .icon-btn:only-child{margin:0px;border-radius:3px} .dataset .details .actions .left .icon-btn{margin-right:2px} -.dataset .details .actions .left:not(:empty){margin-bottom:8px} .dataset .details .actions .left .icon-btn.visualization-btn{margin-left:0px;border-radius:0px 3px 3px 0px;border-right:1px solid #bfbfbf} .dataset .details .actions .right{display:inline-block;float:right}.dataset .details .actions .right .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} .dataset .details .actions .right .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} .dataset .details .actions .right .icon-btn:last-child{margin-left:0px;border-radius:0px 3px 3px 0px} .dataset .details .actions .right .icon-btn:only-child{margin:0px;border-radius:3px} .dataset .details .actions .right .icon-btn{margin-left:2px} +.dataset .details .actions:not(:last-child){margin-bottom:8px} .dataset .details .tags-display{display:none;margin-bottom:8px}.dataset .details .tags-display .select2-container{min-width:0px}.dataset .details .tags-display .select2-container .select2-choices{border-radius:3px} .dataset .details .annotation-display{display:none;margin-bottom:8px}.dataset .details .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line;overflow:auto} .dataset .details .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} diff -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 -r 9b2dc0bd882a0432809f455acce191c333b8df02 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -356,11 +356,6 @@ .icon-btn { margin-right: @icon-btn-margin; } - &:not(:empty) { - // can't use :empty on dataset-actions - will always have left & right, so - // add gap to left (more likely to have children) - .list-item .vertical-spacing; - } // have to reapply here - dropdown wrapped in div .icon-btn.visualization-btn { margin-left: 0px; @@ -375,6 +370,9 @@ margin-left: @icon-btn-margin; } } + &:not(:last-child) { + .list-item .vertical-spacing; + } } //TODO: move these out Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Controller updates for the resubmitted dataset instance state (thanks Carl!)
by commits-noreply＠bitbucket.org 13 Aug '14

13 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d301ac50aa86/ Changeset: d301ac50aa86 User: natefoo Date: 2014-08-12 21:21:40 Summary: Controller updates for the resubmitted dataset instance state (thanks Carl!) Affected #: 2 files diff -r d30b580ffbc5cdb5f9fe8fcefe7261152fab1303 -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -940,10 +940,9 @@ def mark_as_resubmitted( self ): job = self.get_job() self.sa_session.refresh( job ) - # TODO: Enable this code once a UI for resubmitted datasets exists - #for dataset in [ dataset_assoc.dataset for dataset_assoc in job.output_datasets + job.output_library_datasets ]: - # dataset._state = model.Dataset.states.RESUBMITTED - # self.sa_session.add( dataset ) + for dataset in [ dataset_assoc.dataset for dataset_assoc in job.output_datasets + job.output_library_datasets ]: + dataset._state = model.Dataset.states.RESUBMITTED + self.sa_session.add( dataset ) job.state = model.Job.states.RESUBMITTED self.sa_session.add( job ) self.sa_session.flush() diff -r d30b580ffbc5cdb5f9fe8fcefe7261152fab1303 -r d301ac50aa86a94e230d44eb2ae10c6c0e354b88 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -131,15 +131,20 @@ """ api_type = "file" encoded_id = trans.security.encode_id( hda.id ) + # TODO: handle failed_metadata here as well + state = hda.state + if state == trans.app.model.Dataset.states.RESUBMITTED: + state = hda.dataset.state return { 'id' : encoded_id, 'history_id' : encoded_history_id, 'name' : hda.name, 'type' : api_type, - 'state' : hda.state, + 'state' : state, 'deleted': hda.deleted, 'visible': hda.visible, 'purged': hda.purged, + 'resubmitted': hda._state == trans.app.model.Dataset.states.RESUBMITTED, 'hid' : hda.hid, 'history_content_type' : hda.history_content_type, 'url' : url_for( 'history_content_typed', history_id=encoded_history_id, id=encoded_id, type="dataset" ), @@ -157,6 +162,9 @@ hda_dict = self.get_hda_dict( trans, hda ) hda_dict[ 'display_types' ] = self.get_old_display_applications( trans, hda ) hda_dict[ 'display_apps' ] = self.get_display_apps( trans, hda ) + if hda_dict[ 'state' ] == trans.app.model.Dataset.states.RESUBMITTED: + hda_dict[ 'state' ] = hda.dataset.state + hda_dict[ 'resubmitted' ] = True return hda_dict except Exception, exc: # catch error here - returning a briefer hda_dict with an error attribute Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Do not include invalid tools when checking for "orphan" tool dependencies in the Tool Shed.
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d30b580ffbc5/ Changeset: d30b580ffbc5 User: greg Date: 2014-08-12 20:15:00 Summary: Do not include invalid tools when checking for "orphan" tool dependencies in the Tool Shed. Affected #: 1 file diff -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 -r d30b580ffbc5cdb5f9fe8fcefe7261152fab1303 lib/tool_shed/galaxy_install/dependency_display.py --- a/lib/tool_shed/galaxy_install/dependency_display.py +++ b/lib/tool_shed/galaxy_install/dependency_display.py @@ -153,7 +153,7 @@ # Updating should cause no problems here since a tool dependency cannot be included # in both dictionaries. tool_dependencies.update( orphan_tool_dependencies ) - if tool_dependencies and ( tools or invalid_tools ): + if tool_dependencies and tools: for td_key, requirements_dict in tool_dependencies.items(): if td_key == 'set_environment': # "set_environment": [{"name": "R_SCRIPT_PATH", "type": "set_environment"}] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Datset list item: add resubmitted message; pack scripts
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/264657dfe72d/ Changeset: 264657dfe72d User: carlfeberhard Date: 2014-08-12 19:56:26 Summary: Datset list item: add resubmitted message; pack scripts Affected #: 3 files diff -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -35,6 +35,7 @@ /** event listeners */ _setUpListeners : function(){ +//TODO:?? may want to move this to ListItemView (although this is only needed in the *narrow* panel views (current)) // hide the primary actions in the title bar when selectable this.on( 'selectable', function( isSelectable ){ if( isSelectable ){ @@ -207,9 +208,10 @@ /** Defer to the appropo summary rendering fn based on state */ _renderSummary : function(){ - var summaryRenderFn = this.templates.summaries[ this.model.get( 'state' ) ]; + var json = this.model.toJSON(), + summaryRenderFn = this.templates.summaries[ json.state ]; summaryRenderFn = summaryRenderFn || this.templates.summaries.unknown; - return summaryRenderFn( this.model.toJSON(), this ); + return summaryRenderFn( json, this ); }, /** Render the external display application links */ @@ -408,7 +410,22 @@ '<div>', _l( 'The job creating this dataset was cancelled before completion' ), '</div>' ], 'dataset' ); summaryTemplates[ STATES.QUEUED ] = BASE_MVC.wrapTemplate([ - '<div>', _l( 'This job is waiting to run' ), '</div>' + '<div>', + '<% if( dataset.resubmitted ){ %>', + _l( 'The job creating this dataset has been resubmitted is now waiting to run' ), + '<% } else { %>', + _l( 'This job is waiting to run' ), + '<% } %>', + '</div>' + ], 'dataset' ); + summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([ + '<div>', + '<% if( dataset.resubmitted ){ %>', + _l( 'The job creating this dataset has been resubmitted is now running' ), + '<% } else { %>', + _l( 'This job is currently running' ), + '<% } %>', + '</div>' ], 'dataset' ); summaryTemplates[ STATES.UPLOAD ] = BASE_MVC.wrapTemplate([ '<div>', _l( 'This dataset is currently uploading' ), '</div>' @@ -416,9 +433,6 @@ summaryTemplates[ STATES.SETTING_METADATA ] = BASE_MVC.wrapTemplate([ '<div>', _l( 'Metadata is being auto-detected' ), '</div>' ], 'dataset' ); - summaryTemplates[ STATES.RUNNING ] = BASE_MVC.wrapTemplate([ - '<div>', _l( 'This job is currently running' ), '</div>' - ], 'dataset' ); summaryTemplates[ STATES.PAUSED ] = BASE_MVC.wrapTemplate([ '<div>', _l( 'This job is paused. Use the "Resume Paused Jobs" in the history menu to resume' ), '</div>' ], 'dataset' ); diff -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 static/scripts/packed/mvc/collection/collection-li.js --- a/static/scripts/packed/mvc/collection/collection-li.js +++ b/static/scripts/packed/mvc/collection/collection-li.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(h,d,f){var c=d.ListItemView;var a=c.extend({className:c.prototype.className+" dataset-collection",fxSpeed:"fast",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+"(DCListItemView).initialize:",i);c.prototype.initialize.call(this,i)},expand:function(){var i=this;return i._fetchModelDetails().always(function(){i.trigger("expanded",i)})},_renderSubtitle:function(){var i=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return i.text(f("a list of datasets"));case"paired":return i.text(f("a pair of datasets"));case"list:paired":return i.text(f("a list of paired datasets"))}return i},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DCListItemView("+i+")"}});a.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},c.prototype.templates,{titleBar:i})}());var b=c.extend({logger:console,className:c.prototype.className+" dataset-collection-element",fxSpeed:"fast",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log("DCEListItemView.initialize:",i);c.prototype.initialize.call(this,i)},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DCEListItemView("+i+")"}});b.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},c.prototype.templates,{titleBar:i})}());var e=h.DatasetListItemView.extend({className:h.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log("DatasetDCEListItemView.initialize:",i);h.DatasetListItemView.prototype.initialize.call(this,i)},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DatasetDCEListItemView("+i+")"}});e.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},h.DatasetListItemView.prototype.templates,{titleBar:i})}());var g=a.extend({className:a.prototype.className+" dataset-collection-element",_swapNewRender:function(i){a.prototype._swapNewRender.call(this,i);var j=this.model.get("state")||"ok";this.$el.addClass("state-"+j);return this.$el},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"NestedDCDCEListItemView("+i+")"}});return{DCListItemView:a,DCEListItemView:b,DatasetDCEListItemView:e,NestedDCDCEListItemView:g}}); \ No newline at end of file +define(["mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(h,d,f){var c=d.ListItemView;var a=c.extend({className:c.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},fxSpeed:"fast",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log(this+"(DCListItemView).initialize:",i);c.prototype.initialize.call(this,i)},expand:function(){var i=this;return i._fetchModelDetails().always(function(){i.trigger("expanded",i)})},_renderSubtitle:function(){var i=$('<div class="subtitle"></div>');switch(this.model.get("collection_type")){case"list":return i.text(f("a list of datasets"));case"paired":return i.text(f("a pair of datasets"));case"list:paired":return i.text(f("a list of paired datasets"))}return i},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DCListItemView("+i+")"}});a.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- collection.element_identifier || collection.name %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"collection");return _.extend({},c.prototype.templates,{titleBar:i})}());var b=c.extend({logger:console,className:c.prototype.className+" dataset-collection-element",fxSpeed:"fast",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log("DCEListItemView.initialize:",i);c.prototype.initialize.call(this,i)},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DCEListItemView("+i+")"}});b.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>",'<div class="subtitle"></div>',"</div>"],"element");return _.extend({},c.prototype.templates,{titleBar:i})}());var e=h.DatasetListItemView.extend({className:h.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(i){if(i.logger){this.logger=this.model.logger=i.logger}this.log("DatasetDCEListItemView.initialize:",i);h.DatasetListItemView.prototype.initialize.call(this,i)},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"DatasetDCEListItemView("+i+")"}});e.prototype.templates=(function(){var i=d.wrapTemplate(['<div class="title-bar clear" tabindex="0">','<span class="state-icon"></span>','<div class="title">','<span class="name"><%- element.element_identifier %></span>',"</div>","</div>"],"element");return _.extend({},h.DatasetListItemView.prototype.templates,{titleBar:i})}());var g=a.extend({className:a.prototype.className+" dataset-collection-element",_swapNewRender:function(i){a.prototype._swapNewRender.call(this,i);var j=this.model.get("state")||"ok";this.$el.addClass("state-"+j);return this.$el},toString:function(){var i=(this.model)?(this.model+""):("(no model)");return"NestedDCDCEListItemView("+i+")"}});return{DCListItemView:a,DCEListItemView:b,DatasetDCEListItemView:e,NestedDCDCEListItemView:g}}); \ No newline at end of file diff -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 static/scripts/packed/mvc/dataset/dataset-li.js --- a/static/scripts/packed/mvc/dataset/dataset-li.js +++ b/static/scripts/packed/mvc/dataset/dataset-li.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.templates.summaries[this.model.get("state")];f=f||this.templates.summaries.unknown;return f(this.model.toJSON(),this)},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"dataset-params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var g=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var h=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var i={};i[a.OK]=i[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");i[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");i[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");i[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");i[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");i[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");i[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");i[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");i[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");i[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");i[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");i.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:g,details:h,summaries:i,displayApplications:f})}());return{DatasetListItemView:d}}); \ No newline at end of file +define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var e=b.ListItemView;var d=e.extend({className:e.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(f){if(f.logger){this.logger=this.model.logger=f.logger}this.log(this+".initialize:",f);e.prototype.initialize.call(this,f);this.linkTarget=f.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){this.on("selectable",function(f){if(f){this.$(".primary-actions").hide()}else{this.$(".primary-actions").show()}});this.model.on("change",function(g,f){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this);this.on("all",function(f){this.log(f)},this)},_fetchModelDetails:function(){var f=this;if(f.model.inReadyState()&&!f.model.hasDetails()){return f.model.fetch({silent:true})}return jQuery.when()},remove:function(g,h){var f=this;g=g||this.fxSpeed;this.$el.fadeOut(g,function(){Backbone.View.prototype.remove.call(f);if(h){h.call(f)}})},render:function(f){return e.prototype.render.call(this,f)},_swapNewRender:function(f){e.prototype._swapNewRender.call(this,f);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var h=this.model.get("state");if((h===a.NOT_VIEWABLE)||(h===a.DISCARDED)||(!this.model.get("accessible"))){return null}var g={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){g.disabled=true;g.title=c("Cannot display datasets removed from disk")}else{if(h===a.UPLOAD){g.disabled=true;g.title=c("This dataset must finish uploading before it can be viewed")}else{if(h===a.NEW){g.disabled=true;g.title=c("This dataset is not yet viewable")}else{g.title=c("View data");g.href=this.model.urls.display;var f=this;g.onclick=function(i){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+f.model.get("name"),type:"other",content:function(j){var k=new DATA.TabularDataset({id:f.model.get("id")});$.when(k.fetch()).then(function(){DATA.createTabularDatasetChunkedView({model:k,parent_elt:j,embedded:true,height:"100%"})})}});i.preventDefault()}}}}}g.faIcon="fa-eye";return faIconButton(g)},_renderDetails:function(){var f=e.prototype._renderDetails.call(this);f.find(".actions .left").empty().append(this._renderSecondaryActions());f.find(".summary").html(this._renderSummary());f.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(f);return f},_renderSummary:function(){var f=this.model.toJSON(),g=this.templates.summaries[f.state];g=g||this.templates.summaries.unknown;return g(f,this)},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var f=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+f.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(g){return['<li><a href="',f.meta_download+g.file_type,'">',c("Download")," ",g.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},toString:function(){var f=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+f+")"}});d.prototype.templates=(function(){var g=_.extend({},e.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var h=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var i={};i[a.OK]=i[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.data_type ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.data_type %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");i[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");i[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");i[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");i[a.QUEUED]=b.wrapTemplate(["<div>","<% if( dataset.resubmitted ){ %>",c("The job creating this dataset has been resubmitted is now waiting to run"),"<% } else { %>",c("This job is waiting to run"),"<% } %>","</div>"],"dataset");i[a.RUNNING]=b.wrapTemplate(["<div>","<% if( dataset.resubmitted ){ %>",c("The job creating this dataset has been resubmitted is now running"),"<% } else { %>",c("This job is currently running"),"<% } %>","</div>"],"dataset");i[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");i[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");i[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");i[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");i[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");i.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var f=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},e.prototype.templates,{warnings:g,details:h,summaries:i,displayApplications:f})}());return{DatasetListItemView:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: QA, qunit: update HDA, history contents tests
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bdfef8f7d523/ Changeset: bdfef8f7d523 User: carlfeberhard Date: 2014-08-12 18:48:28 Summary: QA, qunit: update HDA, history contents tests Affected #: 2 files diff -r f926988f8e0a480c09d3462002f482b5ac806682 -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 test/qunit/tests/hda-base.js --- a/test/qunit/tests/hda-base.js +++ b/test/qunit/tests/hda-base.js @@ -1,14 +1,13 @@ // This file isn't really testing anything useful yet, it is just testing // (or demonstrating) qunit+backbone interactions. define([ - "mvc/dataset/hda-model", - "mvc/dataset/hda-base", + "mvc/history/hda-model", + "mvc/history/hda-li", "jquery", - "sinon-qunit", - "utils/localization" + "sinon-qunit" ], function( - hdaModel, - hdaBase, + HDA_MODEL, + HDA_BASE, $, sinon ){ @@ -18,10 +17,10 @@ module( "HDA base backbone view tests" ); test( "Base HDA view default construction, initialize", function() { - var hda = new hdaModel.HistoryDatasetAssociation({ + var hda = new HDA_MODEL.HistoryDatasetAssociation({ id : '123' }), - view = new hdaBase.HDABaseView({ model: hda }); + view = new HDA_BASE.HDAListItemView({ model: hda }); strictEqual( view.model, hda ); @@ -30,6 +29,6 @@ equal( view.selected, false ); equal( view.expanded, false ); equal( view.draggable, false ); - equal( view.id(), 'hda-123' ); + equal( view.id(), 'dataset-123' ); }); }); diff -r f926988f8e0a480c09d3462002f482b5ac806682 -r bdfef8f7d52336fbcd8b72ac06c37224ef9b87f5 test/qunit/tests/history_contents_model_tests.js --- a/test/qunit/tests/history_contents_model_tests.js +++ b/test/qunit/tests/history_contents_model_tests.js @@ -1,46 +1,45 @@ // This file isn't really testing anything useful yet, it is just testing // (or demonstrating) qunit+backbone interactions. define([ - "mvc/dataset/hda-model", + "mvc/history/hda-model", "jquery", "sinon-qunit" ], function( - hdaModel, + HDA_MODEL, $, sinon ){ module( "History Contents Model Tests" ); test( "HDA Constructions with Default Attributes", function() { - var hda = new hdaModel.HistoryDatasetAssociation(); - expect( 2 ); + var hda = new HDA_MODEL.HistoryDatasetAssociation({}); equal( hda.get( 'name' ), "(unnamed dataset)" ); equal( hda.get( 'state' ), "new" ); } ); test( "HDA Construction with Supplied Attributes", function() { - var hda = new hdaModel.HistoryDatasetAssociation( { - name: "my dataset", - state: "ok", - } ); - expect( 2 ); - + var hda = new HDA_MODEL.HistoryDatasetAssociation({ + history_content_type : 'dataset', + name: "my dataset", + state: "ok" + }); equal( hda.get( 'name' ), "my dataset" ); equal( hda.get( 'state' ), "ok" ); } ); test( "HDA Deletion", function() { - var hda = new hdaModel.HistoryDatasetAssociation( { - id: "hda1", - history_id: "h1", - deleted: false, - } ); - - // Demonstrate sinon stubbing out of Ajax queries... + var hda = new HDA_MODEL.HistoryDatasetAssociation({ + history_content_type : 'dataset', + id: "hda1", + history_id: "h1", + deleted: false + }); equal( hda.get( 'deleted' ), false ); sinon.stub( $, "ajax" ); - hda.delete(); + hda[ 'delete' ](); equal( hda.get( 'deleted' ), true ); - ok( $.ajax.calledWithMatch( { url: "/api/histories/h1/contents/hda1" } ) ); - } ); -} ); + // to get the url sinon used: + //console.debug( $.ajax.lastCall.args[0].url ) + ok( $.ajax.calledWithMatch( { url: "/api/histories/h1/contents/datasets/hda1" } ) ); + }); +}); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: QA, casperjs: fix selectors changed in 7005608
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f926988f8e0a/ Changeset: f926988f8e0a User: carlfeberhard Date: 2014-08-12 17:42:03 Summary: QA, casperjs: fix selectors changed in 7005608 Affected #: 5 files diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 static/scripts/mvc/collection/collection-li.js --- a/static/scripts/mvc/collection/collection-li.js +++ b/static/scripts/mvc/collection/collection-li.js @@ -16,7 +16,11 @@ //logger : console, className : ListItemView.prototype.className + " dataset-collection", - /** */ + id : function(){ + return [ 'dataset_collection', this.model.get( 'id' ) ].join( '-' ); + }, + + /** jq speed for effects used */ fxSpeed : 'fast', //TODO: ununsed diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -16,6 +16,10 @@ //logger : console, className : _super.prototype.className + " dataset", + //TODO:?? doesn't exactly match an hda's type_id + id : function(){ + return [ 'dataset', this.model.get( 'id' ) ].join( '-' ); + }, /** Set up: instance vars, options, and event handlers */ initialize : function( attributes ){ @@ -240,7 +244,7 @@ // gen. safe to show in all cases return faIconButton({ title : _l( 'View details' ), - classes : 'dataset-params-btn', + classes : 'params-btn', href : this.model.urls.show_params, target : this.linkTarget, faIcon : 'fa-info-circle' diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 test/casperjs/hda-state-tests.js --- a/test/casperjs/hda-state-tests.js +++ b/test/casperjs/hda-state-tests.js @@ -321,7 +321,7 @@ // set state directly through model, wait for re-render //TODO: not ideal to test this this.evaluate( function(){ - return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'new' ); + return Galaxy.currHistoryPanel.model.contents.at( 0 ).set( 'state', 'new' ); }); this.wait( 1000, function(){ this.test.comment( 'HDAs in the "new" state should be well formed' ); @@ -359,7 +359,7 @@ var errorString = 'Blah!'; this.evaluate( function( errorString ){ - return Galaxy.currHistoryPanel.model.hdas.getByHid( 1 ).set( 'error', errorString ); + return Galaxy.currHistoryPanel.model.contents.getByHid( 1 ).set( 'error', errorString ); }, errorString ); // wait for re-render @@ -382,8 +382,8 @@ this.historypanel.thenCollapseHda( uploadSelector, function(){ this.evaluate( function(){ - Galaxy.currHistoryPanel.model.hdas.getByHid( 1 ).unset( 'error' ); - return Galaxy.currHistoryPanel.model.hdas.at( 0 ).set( 'state', 'ok' ); + Galaxy.currHistoryPanel.model.contents.getByHid( 1 ).unset( 'error' ); + return Galaxy.currHistoryPanel.model.contents.at( 0 ).set( 'state', 'ok' ); }); }); this.wait( 1000 ); diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -230,6 +230,7 @@ // broken in webkit w/ jq 1.7 spaceghost.historypanel.waitForHdas( function(){ this.test.comment( 'HDAs can be expanded by clicking on the name' ); + this.debug( this.jsonStr( testUploadInfo ) ); var uploadedSelector = '#' + testUploadInfo.hdaElement.attributes.id; this.click( uploadedSelector + ' ' + this.historypanel.data.selectors.hda.title ); diff -r 3aad77adffba5e3cbb8910ca21387c3effefc429 -r f926988f8e0a480c09d3462002f482b5ac806682 test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -63,7 +63,7 @@ * @returns {Object|null} ElementInfo of the historyItemWrapper found, null if not found */ HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title ){ - var wrapperXpath = xpath( '//span[@class="dataset-name" and contains(text(),"' + title + '")]/../../..' ); + var wrapperXpath = xpath( '//span[@class="name" and contains(text(),"' + title + '")]/../../..' ); return this.spaceghost.elementInfoOrNull( wrapperXpath ); }; @@ -138,9 +138,13 @@ if( state !== 'ok' ){ return false; } var hdaOpacity = this.evaluate( function( name ){ - return $( '.dataset-name:contains("' + name + '")' ).parents( '.hda' ).css( 'opacity' ); + // locate the hda by name and return its opacity + console.debug( name ); + console.debug( $( '.name:contains("' + name + '")' ) ); + console.debug( $( '.name:contains("' + name + '")' ).parents( '.hda' ) ); + return $( '.name:contains("' + name + '")' ).parents( '.dataset' ).css( 'opacity' ); }, hdaName ); - this.debug( 'fading in: ' + hdaOpacity ); + //this.debug( 'fading in: ' + hdaOpacity ); return hdaOpacity >= 1; }, function _then(){ then.call( this, hdaElement ); }, @@ -310,19 +314,19 @@ hdaTitleButtons : { // mixing text and selectors here display : { - selector : '.icon-btn.dataset-display', + selector : '.icon-btn.display-btn', tooltip : 'View data', hrefTpl : '/datasets/%s/display', nodeName : 'a' }, edit : { - selector : '.icon-btn.dataset-edit', + selector : '.icon-btn.edit-btn', tooltip : 'Edit attributes', hrefTpl : '/datasets/%s/edit', nodeName : 'a' }, 'delete' : { - selector : '.icon-btn.dataset-delete', + selector : '.icon-btn.delete-btn', tooltip : 'Delete', hrefTpl : 'javascript:void(0);', nodeName : 'a' @@ -330,19 +334,19 @@ }, hdaPrimaryActionButtons : { download : { - selector : '.icon-btn.dataset-download-btn', + selector : '.icon-btn.download-btn', tooltip : 'Download', hrefTpl : '/datasets/%s/display?to_ext=', nodeName : 'a' }, info : { - selector : '.icon-btn.dataset-params-btn', + selector : '.icon-btn.params-btn', tooltip : 'View details', hrefTpl : '/datasets/%s/show_params', nodeName : 'a' }, rerun : { - selector : '.icon-btn.dataset-rerun-btn', + selector : '.icon-btn.rerun-btn', tooltip : 'Run this job again', hrefTpl : '/tool_runner/rerun?id=%s', nodeName : 'a' @@ -365,7 +369,7 @@ }, hda : { wrapper : { - itemClass : '.hda', + itemClass : '.history-content.dataset', stateClasses : { prefix : 'state-', ok : 'state-ok', @@ -374,18 +378,18 @@ }, errorMessage : '.errormessagesmall', - title : '.dataset-title', - titleButtonArea : '.dataset-primary-actions', - summary : '.dataset-summary', - dbkey : '.dataset-dbkey .value', - info : '.dataset-info', - body : '.dataset-body', + title : '.title', + titleButtonArea : '.primary-actions', + summary : '.summary', + dbkey : '.dbkey .value', + info : '.info', + body : '.details', - primaryActionButtons : '.dataset-actions .left', - secondaryActionButtons : '.dataset-actions .right', + primaryActionButtons : '.actions .left', + secondaryActionButtons : '.actions .right', - undeleteLink : '.dataset-undelete', - purgeLink : '.dataset-purge', + undeleteLink : '.undelete-link', + purgeLink : '.purge-link', peek : '.dataset-peek' } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Update tool_list.py to indicate the correct tool_conf.xml (not sample)
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3aad77adffba/ Changeset: 3aad77adffba User: dannon Date: 2014-08-12 17:28:08 Summary: Update tool_list.py to indicate the correct tool_conf.xml (not sample) Affected #: 1 file diff -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 -r 3aad77adffba5e3cbb8910ca21387c3effefc429 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -1,6 +1,6 @@ import os,sys -#--------read tool_conf.xml.sample to get all the tool xml file names----------- +#--------read tool_conf.xml to get all the tool xml file names----------- onoff = 1 tool_list = [] for line in open("tool_conf.xml", "r"): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456)
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/18e8ddfb9c3c/ Changeset: 18e8ddfb9c3c User: dannon Date: 2014-08-12 17:25:22 Summary: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456) tool_list.py should now use tool_conf.xml not tool_conf.xml.sample Affected #: 1 file diff -r a94473459ebb4749a375420492d6da9a948ccd3a -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -3,7 +3,7 @@ #--------read tool_conf.xml.sample to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml.sample", "r"): +for line in open("tool_conf.xml", "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82a9821e0fbb/ Changeset: 82a9821e0fbb Branch: tool_list_fix User: peterjc Date: 2014-08-12 17:13:05 Summary: Created new branch tool_list_fix Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/24d8995c3568/ Changeset: 24d8995c3568 Branch: tool_list_fix User: peterjc Date: 2014-08-12 17:15:04 Summary: tool_list.py should now use tool_conf.xml not tool_conf.xml.sample See a94473459ebb4749a375420492d6da9a948ccd3a where the rest of the run_functional_tests.sh system was updated. Affected #: 1 file diff -r 82a9821e0fbb3b4c9387152e48be189cc2829a45 -r 24d8995c35689fc42e96d6f02dc222cbf75531ed tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -3,7 +3,7 @@ #--------read tool_conf.xml.sample to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml.sample", "r"): +for line in open("tool_conf.xml", "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: https://bitbucket.org/galaxy/galaxy-central/commits/18e8ddfb9c3c/ Changeset: 18e8ddfb9c3c User: dannon Date: 2014-08-12 17:25:22 Summary: Merged in peterjc/galaxy-central/tool_list_fix (pull request #456) tool_list.py should now use tool_conf.xml not tool_conf.xml.sample Affected #: 1 file diff -r a94473459ebb4749a375420492d6da9a948ccd3a -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 tool_list.py --- a/tool_list.py +++ b/tool_list.py @@ -3,7 +3,7 @@ #--------read tool_conf.xml.sample to get all the tool xml file names----------- onoff = 1 tool_list = [] -for line in open("tool_conf.xml.sample", "r"): +for line in open("tool_conf.xml", "r"): if line.find("<!--") != -1: onoff = 0 if line.find("file") != -1 and onoff==1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History panel: clean up and documentation
by commits-noreply＠bitbucket.org 12 Aug '14

12 Aug '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a94473459ebb/ Changeset: a94473459ebb User: carlfeberhard Date: 2014-08-12 16:45:26 Summary: History panel: clean up and documentation Affected #: 19 files diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-li-edit.js --- a/static/scripts/mvc/collection/collection-li-edit.js +++ b/static/scripts/mvc/collection/collection-li-edit.js @@ -13,7 +13,8 @@ var _super = DC_LI.DCListItemView; /** @class Editing view for DatasetCollectionElement. */ -var DCEListItemEdit = _super.extend({ +var DCEListItemEdit = _super.extend( +/** @lends DCEListItemEdit.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-li.js --- a/static/scripts/mvc/collection/collection-li.js +++ b/static/scripts/mvc/collection/collection-li.js @@ -8,7 +8,8 @@ var ListItemView = BASE_MVC.ListItemView; /** @class Read only view for DatasetCollection. */ -var DCListItemView = ListItemView.extend({ +var DCListItemView = ListItemView.extend( +/** @lends DCListItemView.prototype */{ //TODO: may not be needed /** logger used to record this.log messages, commonly set to console */ @@ -26,7 +27,7 @@ ListItemView.prototype.initialize.call( this, attributes ); }, - /** In this override, don't show`or render any details (no need to do anything here) + /** In this override, don't show or render any details (no need to do anything here) * - currently the parent control will load a panel for this collection over itself * @fires expanded when a body has been expanded */ @@ -87,7 +88,8 @@ //============================================================================== /** @class Read only view for DatasetCollectionElement. */ -var DCEListItemView = ListItemView.extend({ +var DCEListItemView = ListItemView.extend( +/** @lends DCEListItemView.prototype */{ //TODO: this might be expendable - compacted with HDAListItemView /** logger used to record this.log messages, commonly set to console */ @@ -99,7 +101,7 @@ /** jq fx speed for this view */ fxSpeed : 'fast', - /** */ + /** set up */ initialize : function( attributes ){ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } this.log( 'DCEListItemView.initialize:', attributes ); @@ -138,14 +140,15 @@ /** @class Read only view for a DatasetCollectionElement that is also an DatasetAssociation * (a dataset contained in a dataset collection). */ -var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend({ +var DatasetDCEListItemView = DATASET_LI.DatasetListItemView.extend( +/** @lends DatasetDCEListItemView.prototype */{ className : DATASET_LI.DatasetListItemView.prototype.className + " dataset-collection-element", /** logger used to record this.log messages, commonly set to console */ //logger : console, - /** */ + /** set up */ initialize : function( attributes ){ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } this.log( 'DatasetDCEListItemView.initialize:', attributes ); @@ -185,7 +188,8 @@ /** @class Read only view for a DatasetCollectionElement that is also a DatasetCollection * (a nested DC). */ -var NestedDCDCEListItemView = DCListItemView.extend({ +var NestedDCDCEListItemView = DCListItemView.extend( +/** @lends NestedDCDCEListItemView.prototype */{ className : DCListItemView.prototype.className + " dataset-collection-element", diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-model.js --- a/static/scripts/mvc/collection/collection-model.js +++ b/static/scripts/mvc/collection/collection-model.js @@ -47,7 +47,7 @@ * When collection elements are passed from the API, the underlying element is * in a sub-object 'object' (IOW, a DCE representing an HDA will have HDA json in element.object). * This mixin uses the constructor and parse methods to merge that JSON with the DCE attribtues - * effectively changing a DCE from a container to a subclass. + * effectively changing a DCE from a container to a subclass (has a --> is a). */ var DatasetCollectionElementMixin = { @@ -82,7 +82,7 @@ }; //TODO: unused? -/** Concrete class of Generic DatasetCollectionElement */ +/** @class Concrete class of Generic DatasetCollectionElement */ var DatasetCollectionElement = Backbone.Model .extend( BASE_MVC.LoggableMixin ) .extend( DatasetCollectionElementMixin ); @@ -94,7 +94,6 @@ /** @lends DCECollection.prototype */{ model: DatasetCollectionElement, - // comment this out to suppress log output /** logger used to record this.log messages, commonly set to console */ //logger : console, @@ -124,7 +123,10 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, - defaults : _.extend( {}, DATASET_MODEL.DatasetAssociation.prototype.defaults, DatasetCollectionElementMixin.defaults ), + defaults : _.extend( {}, + DATASET_MODEL.DatasetAssociation.prototype.defaults, + DatasetCollectionElementMixin.defaults + ), // because all objects have constructors (as this hashmap would even if this next line wasn't present) // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model @@ -162,7 +164,7 @@ //logger : console, //TODO: unused? - /** */ + /** set up */ initialize : function( attributes, options ){ this.debug( this + '(DatasetDCECollection).initialize:', attributes, options ); DCECollection.prototype.initialize.call( this, attributes, options ); @@ -203,7 +205,7 @@ /** Which class to use for elements */ collectionClass : DCECollection, - /** */ + /** set up: create elements instance var and (on changes to elements) update them */ initialize : function( model, options ){ this.debug( this + '(DatasetCollection).initialize:', model, options, this ); //historyContent.HistoryContent.prototype.initialize.call( this, attrs, options ); @@ -269,6 +271,7 @@ }, // ........................................................................ searchable + /** searchable attributes for collections */ searchAttributes : [ 'name' ], @@ -291,6 +294,7 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, + /** override since we know the collection will only contain datasets */ collectionClass : DatasetDCECollection, //TODO: unused? @@ -368,10 +372,11 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, + /** This is a collection of nested collections */ model: NestedDCDCE, //TODO: unused? - /** */ + /** set up */ initialize : function( attrs, options ){ this.debug( this + '(NestedDCDCECollection).initialize:', attrs, options ); DCECollection.prototype.initialize.call( this, attrs, options ); @@ -394,7 +399,10 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, - /** */ + // because all objects have constructors (as this hashmap would even if this next line wasn't present) + // the constructor in hcontentMixin won't be attached by BASE_MVC.mixin to this model + // - re-apply manually it now + /** This is both a collection and a collection element - call the constructor */ constructor : function( attributes, options ){ this.debug( '\t NestedPairDCDCE.constructor:', attributes, options ); //DatasetCollection.constructor.call( this, attributes, options ); @@ -418,10 +426,11 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, + /** We know this collection is composed of only nested pair collections */ model: NestedPairDCDCE, //TODO: unused? - /** */ + /** set up */ initialize : function( attrs, options ){ this.debug( this + '(NestedPairDCDCECollection).initialize:', attrs, options ); NestedDCDCECollection.prototype.initialize.call( this, attrs, options ); @@ -443,11 +452,11 @@ /** logger used to record this.log messages, commonly set to console */ //logger : console, - // list:paired is the only collection that itself contains collections + /** list:paired is the only collection that itself contains collections */ collectionClass : NestedPairDCDCECollection, //TODO: unused? - /** */ + /** set up */ initialize : function( attributes, options ){ this.debug( this + '(ListPairedDatasetCollection).initialize:', attributes, options ); DatasetCollection.prototype.initialize.call( this, attributes, options ); diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/collection/collection-panel.js --- a/static/scripts/mvc/collection/collection-panel.js +++ b/static/scripts/mvc/collection/collection-panel.js @@ -24,7 +24,9 @@ /** (in ms) that jquery effects will use */ fxSpeed : 'fast', + /** sub view class used for datasets */ DatasetDCEViewClass : DC_LI.DatasetDCEListItemView, + /** sub view class used for nested collections */ NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView, // ......................................................................... SET UP @@ -229,7 +231,7 @@ } }, - /** */ + /** When a sub-collection is clicked, hide the current panel and render the sub-collection in its own panel */ _addCollectionPanel : function( collectionView ){ //TODO: a bit hackish var currPanel = this, @@ -333,9 +335,11 @@ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ -var ListCollectionPanel = CollectionPanel.extend({ +var ListCollectionPanel = CollectionPanel.extend( +/** @lends ListCollectionPanel.prototype */{ //TODO: not strictly needed - due to switch in CollectionPanel._getContentClass + /** sub view class used for datasets */ DatasetDCEViewClass : DC_LI.DatasetDCEListItemView, // ........................................................................ misc @@ -348,7 +352,8 @@ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ -var PairCollectionPanel = ListCollectionPanel.extend({ +var PairCollectionPanel = ListCollectionPanel.extend( +/** @lends PairCollectionPanel.prototype */{ // ........................................................................ misc /** string rep */ @@ -360,9 +365,11 @@ // ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. */ -var ListOfPairsCollectionPanel = CollectionPanel.extend({ +var ListOfPairsCollectionPanel = CollectionPanel.extend( +/** @lends ListOfPairsCollectionPanel.prototype */{ //TODO: not strictly needed - due to switch in CollectionPanel._getContentClass + /** sub view class used for nested collections */ NestedDCDCEViewClass : DC_LI.NestedDCDCEListItemView, // ........................................................................ misc diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/dataset/dataset-model.js --- a/static/scripts/mvc/dataset/dataset-model.js +++ b/static/scripts/mvc/dataset/dataset-model.js @@ -10,7 +10,7 @@ * The DA's are made searchable (by attribute) by mixing in SearchableModelMixin. */ var DatasetAssociation = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( - BASE_MVC.mixin( searchableMixin, { + BASE_MVC.mixin( searchableMixin, /** @lends DatasetAssociation.prototype */{ /** default attributes for a model */ defaults : { @@ -43,8 +43,10 @@ //annotation : '' }, - initialize : function( attrs, options ){ - this.debug( 'Dataset.initialize', attrs, options ); + /** instance vars and listeners */ + initialize : function( attributes, options ){ + this.debug( this + '(Dataset).initialize', attributes, options ); + //!! this state is not in trans.app.model.Dataset.states - set it here - if( !this.get( 'accessible' ) ){ this.set( 'state', STATES.NOT_VIEWABLE ); @@ -62,7 +64,6 @@ var id = this.get( 'id' ); if( !id ){ return {}; } var urls = { -//TODO: how many of these are still used? 'purge' : 'datasets/' + id + '/purge_async', 'display' : 'datasets/' + id + '/display/?preview=True', 'edit' : 'datasets/' + id + '/edit', @@ -146,6 +147,7 @@ return this.save( { deleted: false }, options ); }, + /** remove the file behind this dataset from the filesystem (if permitted) */ purge : function _purge( options ){ //TODO: use, override model.destroy, HDA.delete({ purge: true }) if( this.get( 'purged' ) ){ return jQuery.when(); } @@ -160,7 +162,7 @@ // }, options )); // //xhr.done( function( response ){ - // console.debug( 'response', response ); + // hda.debug( 'response', response ); // //hda.set({ deleted: true, purged: true }); // hda.set( response ); //}); diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/dataset/states.js --- a/static/scripts/mvc/dataset/states.js +++ b/static/scripts/mvc/dataset/states.js @@ -27,8 +27,9 @@ PAUSED : 'paused', /** metadata discovery/setting failed or errored (but otherwise ok) */ FAILED_METADATA : 'failed_metadata', +//TODO: not in trans.app.model.Dataset.states - is in database /** not accessible to the current user (i.e. due to permissions) */ - NOT_VIEWABLE : 'noPermission', // not in trans.app.model.Dataset.states + NOT_VIEWABLE : 'noPermission', /** deleted while uploading */ DISCARDED : 'discarded', /** the tool producing this dataset failed */ diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-li-edit.js --- a/static/scripts/mvc/history/hdca-li-edit.js +++ b/static/scripts/mvc/history/hdca-li-edit.js @@ -7,7 +7,8 @@ var _super = HDCA_LI.HDCAListItemView; /** @class Editing view for HistoryDatasetCollectionAssociation. */ -var HDCAListItemEdit = _super.extend({ +var HDCAListItemEdit = _super.extend( +/** @lends HDCAListItemEdit.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-li.js --- a/static/scripts/mvc/history/hdca-li.js +++ b/static/scripts/mvc/history/hdca-li.js @@ -9,13 +9,12 @@ var _super = DC_LI.DCListItemView; /** @class Read only view for HistoryDatasetCollectionAssociation (a dataset collection inside a history). */ -var HDCAListItemView = _super.extend({ +var HDCAListItemView = _super.extend( +/** @lends HDCAListItemView.prototype */{ /** logger used to record this.log messages, commonly set to console */ //logger : console, -//TODO: not a dataset - /** */ className : _super.prototype.className + " history-content", /** In this override, add the state as a class for use with state-based CSS */ diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/hdca-model.js --- a/static/scripts/mvc/history/hdca-model.js +++ b/static/scripts/mvc/history/hdca-model.js @@ -19,7 +19,6 @@ //============================================================================== /** @class Backbone model for List Dataset Collection within a History. - * @constructs */ var HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend( /** @lends HistoryListDatasetCollection.prototype */{ diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-content-model.js --- a/static/scripts/mvc/history/history-content-model.js +++ b/static/scripts/mvc/history/history-content-model.js @@ -34,20 +34,24 @@ // Build a new id (type_id) that prefixes the history_content_type so the bbone collection can differentiate idAttribute : 'type_id', + /** override constructor to build type_id and insert into original attributes */ constructor : function( attrs, options ){ attrs.type_id = typeIdStr( attrs.history_content_type, attrs.id ); this.debug( 'HistoryContentMixin.constructor:', attrs.type_id ); Backbone.Model.apply( this, arguments ); }, + /** object level fn for building the type_id string */ _typeIdStr : function(){ return typeIdStr( this.get( 'history_content_type' ), this.get( 'id' ) ); }, + /** add listener to re-create type_id when the id changes */ initialize : function( attrs, options ){ this.on( 'change:id', this._createTypeId ); }, + /** set the type_id in the model attributes */ _createTypeId : function(){ this.set( 'type_id', this._typeIdStr() ); }, @@ -90,12 +94,12 @@ return url; }, - /** save this HDA as not visible */ + /** save this content as not visible */ hide : function( options ){ if( !this.get( 'visible' ) ){ return jQuery.when(); } return this.save( { visible: false }, options ); }, - /** save this HDA as visible */ + /** save this content as visible */ unhide : function( options ){ if( this.get( 'visible' ) ){ return jQuery.when(); } return this.save( { visible: true }, options ); @@ -114,6 +118,7 @@ //============================================================================== +//TODO: needed? /** @class (Concrete/non-mixin) base model for content items. */ var HistoryContent = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( HistoryContentMixin ); diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-contents.js --- a/static/scripts/mvc/history/history-contents.js +++ b/static/scripts/mvc/history/history-contents.js @@ -26,7 +26,6 @@ /** since history content is a mix, override model fn into a factory, creating based on history_content_type */ model : function( attrs, options ) { - //console.debug( 'HistoryContents.model:', attrs, options ); //TODO: can we move the type_id stuff here? //attrs.type_id = typeIdStr( attrs ); @@ -70,24 +69,25 @@ }, // ........................................................................ common queries - /** Get the ids of every hda in this collection + /** Get the ids of every item in this collection * @returns array of encoded ids */ ids : function(){ - return this.map( function( hda ){ return hda.get('id'); }); +//TODO: is this still useful since type_id + return this.map( function( item ){ return item.get('id'); }); }, - /** Get hdas that are not ready - * @returns array of HDAs + /** Get contents that are not ready + * @returns array of content models */ notReady : function(){ - return this.filter( function( hda ){ - return !hda.inReadyState(); + return this.filter( function( content ){ + return !content.inReadyState(); }); }, - /** Get the id of every hda in this collection not in a 'ready' state (running). - * @returns an array of hda ids + /** Get the id of every model in this collection not in a 'ready' state (running). + * @returns an array of model ids * @see HistoryDatasetAssociation#inReadyState */ running : function(){ @@ -95,24 +95,26 @@ this.each( function( item ){ var isRunning = !item.inReadyState(); if( isRunning ){ +//TODO: is this still correct since type_id idList.push( item.get( 'id' ) ); } }); return idList; }, - /** Get the hda with the given hid + /** Get the model with the given hid * @param {Int} hid the hid to search for - * @returns {HistoryDatasetAssociation} the hda with the given hid or undefined if not found + * @returns {HistoryDatasetAssociation} the model with the given hid or undefined if not found */ getByHid : function( hid ){ - return _.first( this.filter( function( hda ){ return hda.get( 'hid' ) === hid; }) ); + return _.first( this.filter( function( content ){ return content.get( 'hid' ) === hid; }) ); }, - /** Get every 'shown' hda in this collection based on show_deleted/hidden - * @param {Boolean} show_deleted are we showing deleted hdas? - * @param {Boolean} show_hidden are we showing hidden hdas? - * @returns array of hda models + //TODO:?? this may belong in the containing view + /** Get every 'shown' model in this collection based on show_deleted/hidden + * @param {Boolean} show_deleted are we showing deleted content? + * @param {Boolean} show_hidden are we showing hidden content? + * @returns array of content models * @see HistoryDatasetAssociation#isVisible */ getVisible : function( show_deleted, show_hidden, filters ){ @@ -131,13 +133,13 @@ return filteredHdas; }, - /** return true if any hdas don't have details */ + /** return true if any contents don't have details */ haveDetails : function(){ - return this.all( function( hda ){ return hda.hasDetails(); }); + return this.all( function( content ){ return content.hasDetails(); }); }, // ........................................................................ ajax - /** fetch detailed model data for all HDAs in this collection */ + /** fetch detailed model data for all contents in this collection */ fetchAllDetails : function( options ){ options = options || {}; var detailsFlag = { details: 'all' }; @@ -145,8 +147,8 @@ return this.fetch( options ); }, - /** using a queue, perform hdaAjaxFn on each of the hdas in this collection */ - ajaxQueue : function( hdaAjaxFn, options ){ + /** using a queue, perform ajaxFn on each of the models in this collection */ + ajaxQueue : function( ajaxFn, options ){ var deferred = jQuery.Deferred(), startingLength = this.length, responses = []; @@ -157,12 +159,12 @@ } // use reverse order (stylistic choice) - var ajaxFns = this.chain().reverse().map( function( hda, i ){ + var ajaxFns = this.chain().reverse().map( function( content, i ){ return function(){ - var xhr = hdaAjaxFn.call( hda, options ); + var xhr = ajaxFn.call( content, options ); // if successful, notify using the deferred to allow tracking progress xhr.done( function( response ){ - deferred.notify({ curr: i, total: startingLength, response: response, model: hda }); + deferred.notify({ curr: i, total: startingLength, response: response, model: content }); }); // (regardless of previous error or success) if not last ajax call, shift and call the next // if last fn, resolve deferred @@ -183,17 +185,18 @@ }, // ........................................................................ sorting/filtering - /** return a new collection of HDAs whose attributes contain the substring matchesWhat */ + /** return a new collection of contents whose attributes contain the substring matchesWhat */ matches : function( matchesWhat ){ - return this.filter( function( hda ){ - return hda.matches( matchesWhat ); + return this.filter( function( content ){ + return content.matches( matchesWhat ); }); }, // ........................................................................ misc + /** override to get a correct/smarter merge when incoming data is partial */ set : function( models, options ){ // arrrrrrrrrrrrrrrrrg... - // override to get a correct/smarter merge when incoming data is partial (e.g. stupid backbone) + // (e.g. stupid backbone) // w/o this partial models from the server will fill in missing data with model defaults // and overwrite existing data on the client // see Backbone.Collection.set and _prepareModel @@ -213,7 +216,7 @@ Backbone.Collection.prototype.set.call( this, models, options ); }, - /** Convert this ad-hoc collection of HDAs to a formal collection tracked + /** Convert this ad-hoc collection of hdas to a formal collection tracked by the server. **/ promoteToHistoryDatasetCollection : function _promote( history, collection_type, options ){ diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-annotated.js --- a/static/scripts/mvc/history/history-panel-annotated.js +++ b/static/scripts/mvc/history/history-panel-annotated.js @@ -23,7 +23,7 @@ * @constructs */ var AnnotatedHistoryPanel = _super.extend( -/** @lends HistoryPanel.prototype */{ +/** @lends AnnotatedHistoryPanel.prototype */{ /** logger used to record this.log messages, commonly set to console */ // comment this out to suppress log output diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -7,7 +7,8 @@ // ============================================================================ /** session storage for history panel preferences (and to maintain state) */ -var HistoryPanelPrefs = BASE_MVC.SessionStorageModel.extend({ +var HistoryPanelPrefs = BASE_MVC.SessionStorageModel.extend( +/** @lends HistoryPanelPrefs.prototype */{ defaults : { /** is the panel currently showing the search/filter controls? */ searching : false, diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel-edit.js --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -333,9 +333,9 @@ // maintain a list of hdas that are selected hdaView.on( 'selected', function( hdaView, event ){ if( !event ){ return; } - //console.debug( 'selected', event ); + //this.debug( 'selected', event ); var selectedIds = []; - //console.debug( historyView.lastSelectedViewId, historyView.hdaViews[ historyView.lastSelectedViewId ] ); + //this.debug( historyView.lastSelectedViewId, historyView.hdaViews[ historyView.lastSelectedViewId ] ); // shift will select a range, but not set lastSelectedViewId if( ( event.shiftKey ) @@ -348,19 +348,19 @@ } else { var id = hdaView.model.id; historyView.lastSelectedViewId = id; - //console.debug( 'lastSelectedViewId:', historyView.lastSelectedViewId ); + //this.debug( 'lastSelectedViewId:', historyView.lastSelectedViewId ); selectedIds = [ id ]; } - //console.debug( 'selectedIds:', selectedIds ); + //this.debug( 'selectedIds:', selectedIds ); historyView.selectedHdaIds = _.union( historyView.selectedHdaIds, selectedIds ); //TODO: might want to use getSelectedHdaViews instead managing these lists with ops - //console.debug( 'selected', historyView.selectedHdaIds ); + //this.debug( 'selected', historyView.selectedHdaIds ); }); hdaView.on( 'de-selected', function( hdaView, event ){ - //console.debug( 'de-selected', event ); + //this.debug( 'de-selected', event ); var id = hdaView.model.id; historyView.selectedHdaIds = _.without( historyView.selectedHdaIds, id ); - //console.debug( 'de-selected', historyView.selectedHdaIds ); + //this.debug( 'de-selected', historyView.selectedHdaIds ); }); }, diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -8,7 +8,9 @@ ], function( HISTORY_MODEL, HDA_LI, HDCA_LI, USER, BASE_MVC, _l ){ // ============================================================================ /** session storage for individual history preferences */ -var HistoryPrefs = BASE_MVC.SessionStorageModel.extend({ +var HistoryPrefs = BASE_MVC.SessionStorageModel.extend( +/** @lends HistoryPrefs.prototype */{ + defaults : { //TODO:?? expandedHdas to array? expandedHdas : {}, @@ -85,6 +87,7 @@ /** class to use for constructing the HDA views */ HDAViewClass : HDA_LI.HDAListItemView, + /** class to use for constructing the HDCA views */ HDCAViewClass : HDCA_LI.HDCAListItemView, tagName : 'div', @@ -753,17 +756,17 @@ this.storage.get( 'show_hidden' ), this.filters ).each( function( hda ){ - //console.debug( 'checking: ', hda.get( 'name' ) ); + //panel.debug( 'checking: ', hda.get( 'name' ) ); if( withinSet ){ - //console.debug( '\t\t adding: ', hda.get( 'name' ) ); + //panel.debug( '\t\t adding: ', hda.get( 'name' ) ); set.push( panel.hdaViews[ hda.id ] ); if( hda === viewA.model || hda === viewB.model ){ - //console.debug( '\t found last: ', hda.get( 'name' ) ); + //panel.debug( '\t found last: ', hda.get( 'name' ) ); withinSet = false; } } else { if( hda === viewA.model || hda === viewB.model ){ - //console.debug( 'found first: ', hda.get( 'name' ) ); + //panel.debug( 'found first: ', hda.get( 'name' ) ); withinSet = true; set.push( panel.hdaViews[ hda.id ] ); } diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/collection/collection-panel.js --- a/static/scripts/packed/mvc/collection/collection-panel.js +++ b/static/scripts/packed/mvc/collection/collection-panel.js @@ -1,1 +1,1 @@ -define(["mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(h,f,a,e){var d=Backbone.View.extend(a.LoggableMixin).extend({tagName:"div",className:"dataset-collection-panel",fxSpeed:"fast",DatasetDCEViewClass:f.DatasetDCEListItemView,NestedDCDCEViewClass:f.NestedDCDCEListItemView,initialize:function(i){i=i||{};if(i.logger){this.logger=i.logger}this.log(this+".initialize:",i);this.linkTarget=i.linkTarget||"_blank";this.hasUser=i.hasUser;this.panelStack=[];this.parentName=i.parentName;window.collectionPanel=this},_setUpListeners:function(){this.on("all",function(i){this.log(this+"",arguments)},this);return this},_setUpModelEventHandlers:function(){return this},render:function(k,l){this.log("render:",k,l);k=(k===undefined)?(this.fxSpeed):(k);var i=this,j;if(!this.model){return this}j=this.renderModel();$(i).queue("fx",[function(m){if(k&&i.$el.is(":visible")){i.$el.fadeOut(k,m)}else{m()}},function(m){i.$el.empty();if(j){i.$el.append(j.children())}m()},function(m){if(k&&!i.$el.is(":visible")){i.$el.fadeIn(k,m)}else{m()}},function(m){if(l){l.call(this)}i.trigger("rendered",this);m()}]);return this},renderModel:function(){var k=this.model.get("collection_type")||this.model.object.get("collection_type"),j=_.extend(this.model.toJSON(),{parentName:this.parentName,type:k}),i=$("<div/>").append(this.templates.panel(j));this._setUpBehaviours(i);this.renderContents(i);return i},_setUpBehaviours:function(i){i=i||this.$el;i.find("[title]").tooltip({placement:"bottom"});return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(i){return(i||this.$el).find(".datasets-list")},renderContents:function(j){j=j||this.$el;this.warn(this+".renderContents:, model:",this.model);var i=this,l={},k=this.model.getVisibleContents();this.$datasetsList(j).empty();if(k&&k.length){k.each(function(n){var o=n.id,m=i._createContentView(n);l[o]=m;i._attachContentView(m.render(),j)})}this.contentViews=l;return this.contentViews},_createContentView:function(k){var j=null,i=this._getContentClass(k);j=new i({model:k,linkTarget:this.linkTarget,hasUser:this.hasUser,logger:this.logger});this._setUpContentListeners(j);return j},_getContentClass:function(i){switch(i.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",i.get("element_type"))},_setUpContentListeners:function(j){var i=this;if(j.model.get("element_type")==="dataset_collection"){j.on("expanded",function(k){i.info("expanded",k);i._addCollectionPanel(k)})}},_addCollectionPanel:function(k){var l=this,i=k.model;var j=new c({model:i,parentName:this.model.get("name"),linkTarget:this.linkTarget});l.panelStack.push(j);l.$(".controls").add(".datasets-list").hide();l.$el.append(j.$el);j.on("close",function(){l.render();k.collapse();l.panelStack.pop()});if(!j.model.hasDetails()){var m=j.model.fetch();m.done(function(){j.render()})}else{j.render()}},_attachContentView:function(k,j){j=j||this.$el;var i=this.$datasetsList(j);i.append(k.$el);return this},events:{"click .navigation .back":"close"},close:function(i){this.$el.remove();this.trigger("close")},toString:function(){return"CollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates=d.prototype.templates=(function(){var i=_.template(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',e("Back to "),"<%- collection.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.type === "list" ){ %>',e("a list of datasets"),'<% } else if( collection.type === "paired" ){ %>',e("a pair of datasets"),'<% } else if( collection.type === "list:paired" ){ %>',e("a list of paired datasets"),"<% } %>","</div>","</div>","</div>",'<div class="datasets-list"></div>'].join(""));return{panel:function(j){return i({_l:e,collection:j})}}}());var b=d.extend({DatasetDCEViewClass:f.DatasetDCEListItemView,toString:function(){return"ListCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var c=b.extend({toString:function(){return"PairCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var g=d.extend({NestedDCDCEViewClass:f.NestedDCDCEListItemView,toString:function(){return"ListOfPairsCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CollectionPanel:d,ListCollectionPanel:b,PairCollectionPanel:c,ListOfPairsCollectionPanel:g}}); \ No newline at end of file +define(["mvc/collection/collection-model","mvc/collection/collection-li","mvc/base-mvc","utils/localization"],function(h,f,a,e){var d=Backbone.View.extend(a.LoggableMixin).extend({tagName:"div",className:"dataset-collection-panel",fxSpeed:"fast",DatasetDCEViewClass:f.DatasetDCEListItemView,NestedDCDCEViewClass:f.NestedDCDCEListItemView,initialize:function(i){i=i||{};if(i.logger){this.logger=i.logger}this.log(this+".initialize:",i);this.linkTarget=i.linkTarget||"_blank";this.hasUser=i.hasUser;this.panelStack=[];this.parentName=i.parentName},_setUpListeners:function(){this.on("all",function(i){this.log(this+"",arguments)},this);return this},_setUpModelEventHandlers:function(){return this},render:function(k,l){this.log("render:",k,l);k=(k===undefined)?(this.fxSpeed):(k);var i=this,j;if(!this.model){return this}j=this.renderModel();$(i).queue("fx",[function(m){if(k&&i.$el.is(":visible")){i.$el.fadeOut(k,m)}else{m()}},function(m){i.$el.empty();if(j){i.$el.append(j.children())}m()},function(m){if(k&&!i.$el.is(":visible")){i.$el.fadeIn(k,m)}else{m()}},function(m){if(l){l.call(this)}i.trigger("rendered",this);m()}]);return this},renderModel:function(){var k=this.model.get("collection_type")||this.model.object.get("collection_type"),j=_.extend(this.model.toJSON(),{parentName:this.parentName,type:k}),i=$("<div/>").append(this.templates.panel(j));this._setUpBehaviours(i);this.renderContents(i);return i},_setUpBehaviours:function(i){i=i||this.$el;i.find("[title]").tooltip({placement:"bottom"});return this},$container:function(){return(this.findContainerFn)?(this.findContainerFn.call(this)):(this.$el.parent())},$datasetsList:function(i){return(i||this.$el).find(".datasets-list")},renderContents:function(j){j=j||this.$el;this.warn(this+".renderContents:, model:",this.model);var i=this,l={},k=this.model.getVisibleContents();this.$datasetsList(j).empty();if(k&&k.length){k.each(function(n){var o=n.id,m=i._createContentView(n);l[o]=m;i._attachContentView(m.render(),j)})}this.contentViews=l;return this.contentViews},_createContentView:function(k){var j=null,i=this._getContentClass(k);j=new i({model:k,linkTarget:this.linkTarget,hasUser:this.hasUser,logger:this.logger});this._setUpContentListeners(j);return j},_getContentClass:function(i){switch(i.get("element_type")){case"hda":return this.DatasetDCEViewClass;case"dataset_collection":return this.NestedDCDCEViewClass}throw new TypeError("Unknown element type:",i.get("element_type"))},_setUpContentListeners:function(j){var i=this;if(j.model.get("element_type")==="dataset_collection"){j.on("expanded",function(k){i.info("expanded",k);i._addCollectionPanel(k)})}},_addCollectionPanel:function(k){var l=this,i=k.model;var j=new c({model:i,parentName:this.model.get("name"),linkTarget:this.linkTarget});l.panelStack.push(j);l.$(".controls").add(".datasets-list").hide();l.$el.append(j.$el);j.on("close",function(){l.render();k.collapse();l.panelStack.pop()});if(!j.model.hasDetails()){var m=j.model.fetch();m.done(function(){j.render()})}else{j.render()}},_attachContentView:function(k,j){j=j||this.$el;var i=this.$datasetsList(j);i.append(k.$el);return this},events:{"click .navigation .back":"close"},close:function(i){this.$el.remove();this.trigger("close")},toString:function(){return"CollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates=d.prototype.templates=(function(){var i=_.template(['<div class="controls">','<div class="navigation">','<a class="back" href="javascript:void(0)">','<span class="fa fa-icon fa-angle-left"></span>',e("Back to "),"<%- collection.parentName %>","</a>","</div>",'<div class="title">','<div class="name"><%- collection.name || collection.element_identifier %></div>','<div class="subtitle">','<% if( collection.type === "list" ){ %>',e("a list of datasets"),'<% } else if( collection.type === "paired" ){ %>',e("a pair of datasets"),'<% } else if( collection.type === "list:paired" ){ %>',e("a list of paired datasets"),"<% } %>","</div>","</div>","</div>",'<div class="datasets-list"></div>'].join(""));return{panel:function(j){return i({_l:e,collection:j})}}}());var b=d.extend({DatasetDCEViewClass:f.DatasetDCEListItemView,toString:function(){return"ListCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var c=b.extend({toString:function(){return"PairCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});var g=d.extend({NestedDCDCEViewClass:f.NestedDCDCEListItemView,toString:function(){return"ListOfPairsCollectionPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CollectionPanel:d,ListCollectionPanel:b,PairCollectionPanel:c,ListOfPairsCollectionPanel:g}}); \ No newline at end of file diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/dataset/dataset-model.js --- a/static/scripts/packed/mvc/dataset/dataset-model.js +++ b/static/scripts/packed/mvc/dataset/dataset-model.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var f=b.SearchableModelMixin;var e=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(f,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(h,g){this.debug("Dataset.initialize",h,g);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var i=this.get("id");if(!i){return{}}var h={purge:"datasets/"+i+"/purge_async",display:"datasets/"+i+"/display/?preview=True",edit:"datasets/"+i+"/edit",download:"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+i,rerun:"tool_runner/rerun?id="+i,show_params:"datasets/"+i+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};var g=(galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(h,function(k,j){h[j]=g+k});this.urls=h;return h},_setUpListeners:function(){this.on("change:state",function(h,g){this.log(this+" has changed state:",h,g);if(this.inReadyState()){this.trigger("state:ready",h,g,this.previous("state"))}});this.on("change:id change:file_ext",function(g){this._generateUrls()})},toJSON:function(){var g=Backbone.Model.prototype.toJSON.call(this);return _.extend(g,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var g=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||g)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function(g){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},g)},undelete:function(g){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},g)},purge:function d(g){if(this.get("purged")){return jQuery.when()}g=g||{};g.url=this.urls.purge;var h=this,i=jQuery.ajax(g);i.done(function(l,j,k){h.set({deleted:true,purged:true})});i.fail(function(n,j,m){var k=c("Unable to purge dataset");var l=("Removal of datasets by users is not allowed in this Galaxy instance");if(n.responseJSON&&n.responseJSON.error){k=n.responseJSON.error}else{if(n.responseText.indexOf(l)!==-1){k=l}}n.responseText=k;h.trigger("error",h,n,g,c(k),{error:k})});return i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var g=this.get("id")||"";if(this.get("name")){g='"'+this.get("name")+'",'+g}return"Dataset("+g+")"}}));return{DatasetAssociation:e}}); \ No newline at end of file +define(["mvc/dataset/states","mvc/base-mvc","utils/localization"],function(a,b,c){var f=b.SearchableModelMixin;var e=Backbone.Model.extend(b.LoggableMixin).extend(b.mixin(f,{defaults:{state:a.NEW,deleted:false,purged:false,name:"(unnamed dataset)",accessible:true,data_type:"",file_ext:"",file_size:0,meta_files:[],misc_blurb:"",misc_info:"",tags:[]},initialize:function(g,h){this.debug(this+"(Dataset).initialize",g,h);if(!this.get("accessible")){this.set("state",a.NOT_VIEWABLE)}this.urls=this._generateUrls();this._setUpListeners()},_generateUrls:function(){var i=this.get("id");if(!i){return{}}var h={purge:"datasets/"+i+"/purge_async",display:"datasets/"+i+"/display/?preview=True",edit:"datasets/"+i+"/edit",download:"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:"dataset/errors?id="+i,rerun:"tool_runner/rerun?id="+i,show_params:"datasets/"+i+"/show_params",visualization:"visualization",meta_download:"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};var g=(galaxy_config&&galaxy_config.root)?(galaxy_config.root):("/");_.each(h,function(k,j){h[j]=g+k});this.urls=h;return h},_setUpListeners:function(){this.on("change:state",function(h,g){this.log(this+" has changed state:",h,g);if(this.inReadyState()){this.trigger("state:ready",h,g,this.previous("state"))}});this.on("change:id change:file_ext",function(g){this._generateUrls()})},toJSON:function(){var g=Backbone.Model.prototype.toJSON.call(this);return _.extend(g,{urls:this.urls})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},inReadyState:function(){var g=_.contains(a.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||g)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function(g){if(this.get("deleted")){return jQuery.when()}return this.save({deleted:true},g)},undelete:function(g){if(!this.get("deleted")||this.get("purged")){return jQuery.when()}return this.save({deleted:false},g)},purge:function d(g){if(this.get("purged")){return jQuery.when()}g=g||{};g.url=this.urls.purge;var h=this,i=jQuery.ajax(g);i.done(function(l,j,k){h.set({deleted:true,purged:true})});i.fail(function(n,j,m){var k=c("Unable to purge dataset");var l=("Removal of datasets by users is not allowed in this Galaxy instance");if(n.responseJSON&&n.responseJSON.error){k=n.responseJSON.error}else{if(n.responseText.indexOf(l)!==-1){k=l}}n.responseText=k;h.trigger("error",h,n,g,c(k),{error:k})});return i},searchAttributes:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],searchAliases:{title:"name",format:"file_ext",database:"genome_build",blurb:"misc_blurb",description:"misc_blurb",info:"misc_info",tag:"tags"},toString:function(){var g=this.get("id")||"";if(this.get("name")){g='"'+this.get("name")+'",'+g}return"Dataset("+g+")"}}));return{DatasetAssociation:e}}); \ No newline at end of file diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/history/history-contents.js --- a/static/scripts/packed/mvc/history/history-contents.js +++ b/static/scripts/packed/mvc/history/history-contents.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(k,j){var i=jQuery.Deferred(),h=this.length,m=[];if(!h){i.resolve([]);return i}var l=this.chain().reverse().map(function(o,n){return function(){var p=k.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){m.push(q);if(l.length){l.shift()()}else{i.resolve(m)}})}}).value();l.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file +define(["mvc/history/history-content-model","mvc/history/hda-model","mvc/history/hdca-model","mvc/base-mvc","utils/localization"],function(g,e,b,a,c){var f=Backbone.Collection.extend(a.LoggableMixin).extend({model:function(i,h){if(i.history_content_type==="dataset"){return new e.HistoryDatasetAssociation(i,h)}else{if(i.history_content_type==="dataset_collection"){switch(i.collection_type){case"list":return new b.HistoryListDatasetCollection(i,h);case"paired":return new b.HistoryPairDatasetCollection(i,h);case"list:paired":return new b.HistoryListPairedDatasetCollection(i,h)}throw new TypeError("Unknown collection_type: "+i.collection_type)}}throw new TypeError("Unknown history_content_type: "+i.history_content_type)},initialize:function(i,h){h=h||{};this.historyId=h.historyId;this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(h){return h.get("id")})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(j){var i=!j.inReadyState();if(i){h.push(j.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,k,j){j=j||[];this.debug("checking isVisible");var i=new f(this.filter(function(l){return l.isVisible(h,k)}));_.each(j,function(l){if(!_.isFunction(l)){return}i=new f(i.filter(l))});return i},haveDetails:function(){return this.all(function(h){return h.hasDetails()})},fetchAllDetails:function(i){i=i||{};var h={details:"all"};i.data=(i.data)?(_.extend(i.data,h)):(h);return this.fetch(i)},ajaxQueue:function(m,j){var i=jQuery.Deferred(),h=this.length,l=[];if(!h){i.resolve([]);return i}var k=this.chain().reverse().map(function(o,n){return function(){var p=m.call(o,j);p.done(function(q){i.notify({curr:n,total:h,response:q,model:o})});p.always(function(q){l.push(q);if(k.length){k.shift()()}else{i.resolve(l)}})}}).value();k.shift()();return i},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(m){var l=m.attributes||m,n=g.typeIdStr(l.history_content_type,l.id),o=i.get(n);if(!o){return m}var k=o.toJSON();_.extend(k,m);return k});Backbone.Collection.prototype.set.call(this,j,h)},promoteToHistoryDatasetCollection:function d(m,k,i){i=i||{};i.url=this.url();i.type="POST";var o=k;var l=[],h=null;if(k==="list"){this.chain().each(function(r){var p=r.attributes.name;var s=r.get("id");var q=r.attributes.history_content_type;if(q==="dataset"){if(o!=="list"){this.log("Invalid collection type")}l.push({name:p,src:"hda",id:s})}else{if(o==="list"){o="list:"+r.attributes.collection_type}else{if(o!=="list:"+r.attributes.collection_type){this.log("Invalid collection type")}}l.push({name:p,src:"hdca",id:s})}});h="New Dataset List"}else{if(k==="paired"){var j=this.ids();if(j.length!==2){}l.push({name:"forward",src:"hda",id:j[0]});l.push({name:"reverse",src:"hda",id:j[1]});h="New Dataset Pair"}}i.data={type:"dataset_collection",name:h,collection_type:o,element_identifiers:JSON.stringify(l)};var n=jQuery.ajax(i);n.done(function(r,p,q){m.refresh()});n.fail(function(r,p,q){if(r.responseJSON&&r.responseJSON.error){error=r.responseJSON.error}else{error=r.responseJSON}r.responseText=error});return n},print:function(){var h=this;h.each(function(i){h.debug(i);if(i.elements){h.debug("\t elements:",i.elements)}})},toString:function(){return(["HistoryContents(",[this.historyId,this.length].join(),")"].join(""))}});return{HistoryContents:f}}); \ No newline at end of file diff -r 588c521575605b698ee15376f3b919f6a2cda20c -r a94473459ebb4749a375420492d6da9a948ccd3a static/scripts/packed/mvc/history/history-panel-annotated.js --- a/static/scripts/packed/mvc/history/history-panel-annotated.js +++ b/static/scripts/packed/mvc/history/history-panel-annotated.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-panel","mvc/history/hda-li","utils/localization"],function(e,b,a){var d=e.ReadOnlyHistoryPanel;var c=d.extend({className:"annotated-history-panel",HDAViewClass:b.HDAReadonlyListItemView,renderModel:function(){this.$el.addClass(this.className);var h=d.prototype.renderModel.call(this),f=this.$datasetsList(h),g=$("<table/>").addClass("datasets-list datasets-table");g.append(f.children());f.replaceWith(g);h.find(".history-subtitle").after(this.renderHistoryAnnotation());h.find(".history-search-btn").hide();h.find(".history-controls").after(h.find(".history-search-controls").show());return h},renderHistoryAnnotation:function(){var f=this.model.get("annotation");if(!f){return null}return $(['<div class="history-annotation">',f,"</div>"].join(""))},renderHdas:function(g){g=g||this.$el;var f=d.prototype.renderHdas.call(this,g);this.$datasetsList(g).prepend($("<tr/>").addClass("headers").append([$("<th/>").text(a("Dataset")),$("<th/>").text(a("Annotation"))]));return f},attachContentView:function(i,g){g=g||this.$el;var j=_.find(i.el.classList,function(k){return(/^state\-/).test(k)}),f=i.model.get("annotation")||"",h=$("<tr/>").addClass("dataset-row").append([$("<td/>").addClass("dataset-container").append(i.$el).addClass(j?j.replace("-","-color-"):""),$("<td/>").addClass("additional-info").text(f)]);this.$datasetsList(g).append(h)},events:_.extend(_.clone(d.prototype.events),{"click tr":function(f){$(f.currentTarget).find(".dataset-title-bar").click()},"click .icon-btn":function(f){f.stopPropagation()}}),toString:function(){return"AnnotatedHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{AnnotatedHistoryPanel:c}}); \ No newline at end of file +define(["mvc/history/history-panel","mvc/history/hda-li","utils/localization"],function(e,b,a){var d=e.ReadOnlyHistoryPanel;var c=d.extend({className:"annotated-history-panel",renderModel:function(){this.$el.addClass(this.className);var h=d.prototype.renderModel.call(this),f=this.$datasetsList(h),g=$("<table/>").addClass("datasets-list datasets-table");g.append(f.children());f.replaceWith(g);h.find(".history-subtitle").after(this.renderHistoryAnnotation());h.find(".history-search-btn").hide();h.find(".history-controls").after(h.find(".history-search-controls").show());return h},renderHistoryAnnotation:function(){var f=this.model.get("annotation");if(!f){return null}return $(['<div class="history-annotation">',f,"</div>"].join(""))},renderHdas:function(g){g=g||this.$el;var f=d.prototype.renderHdas.call(this,g);this.$datasetsList(g).prepend($("<tr/>").addClass("headers").append([$("<th/>").text(a("Dataset")),$("<th/>").text(a("Annotation"))]));return f},attachContentView:function(i,g){g=g||this.$el;var j=_.find(i.el.classList,function(k){return(/^state\-/).test(k)}),f=i.model.get("annotation")||"",h=$("<tr/>").addClass("dataset-row").append([$("<td/>").addClass("dataset-container").append(i.$el).addClass(j?j.replace("-","-color-"):""),$("<td/>").addClass("additional-info").text(f)]);this.$datasetsList(g).append(h)},events:_.extend(_.clone(d.prototype.events),{"click tr":function(f){$(f.currentTarget).find(".dataset-title-bar").click()},"click .icon-btn":function(f){f.stopPropagation()}}),toString:function(){return"AnnotatedHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{AnnotatedHistoryPanel:c}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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