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commit/galaxy-central: carlfeberhard: Fix TypeDef error in history panel by adding sanity check for tags/annotations being open (Thanks, Aysam)
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c85f8fb5d63e/ Changeset: c85f8fb5d63e User: carlfeberhard Date: 2014-02-18 22:40:23 Summary: Fix TypeDef error in history panel by adding sanity check for tags/annotations being open (Thanks, Aysam) Affected #: 2 files diff -r 82d6ee82d5d4714eefdbce041f6c983a806a58d7 -r c85f8fb5d63e667b63e10cdce518254f56002f55 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -44,6 +44,11 @@ /** selected hda ids */ this.selectedHdaIds = []; + /** editor for tags - sub-view */ + this.tagsEditor = null; + /** editor for annotations - sub-view */ + this.annotationEditor = null; + // states/modes the panel can be in /** is the panel currently showing the dataset selection controls? */ this.selecting = attributes.selecting || false; @@ -250,8 +255,8 @@ selectable : this.selecting, hasUser : this.model.ownedByCurrUser(), logger : this.logger, - tagsEditorShown : !this.tagsEditor.isHidden(), - annotationEditorShown : !this.annotationEditor.isHidden() + tagsEditorShown : ( this.tagsEditor && !this.tagsEditor.isHidden() ), + annotationEditorShown : ( this.annotationEditor && !this.annotationEditor.isHidden() ) }); this._setUpHdaListeners( hdaView ); return hdaView; diff -r 82d6ee82d5d4714eefdbce041f6c983a806a58d7 -r c85f8fb5d63e667b63e10cdce518254f56002f55 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:!this.tagsEditor.isHidden(),annotationEditorShown:!this.annotationEditor.isHidden()});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.isHidden()),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.isHidden())});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ 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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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/33812bcdc523/ Changeset: 33812bcdc523 User: carlfeberhard Date: 2014-02-18 21:11:48 Summary: History panel: begin process of breaking up panel into more focused prototypes Affected #: 11 files diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -887,10 +887,13 @@ history_dictionary = {} hda_dictionaries = [] + user_is_owner = False try: history_to_view = self.get_history( trans, id, False ) if not history_to_view: return trans.show_error_message( "The specified history does not exist." ) + if history_to_view.user == trans.user: + user_is_owner = True # Admin users can view any history if( ( history_to_view.user != trans.user ) @@ -925,7 +928,7 @@ + 'Please contact a Galaxy administrator if the problem persists.' ) return trans.fill_template_mako( "history/view.mako", - history=history_dictionary, hdas=hda_dictionaries, + history=history_dictionary, hdas=hda_dictionaries, user_is_owner=user_is_owner, show_deleted=show_deleted, show_hidden=show_hidden, use_panels=use_panels ) @web.expose @@ -941,9 +944,8 @@ # Security check raises error if user cannot access history. self.security_check( trans, history, False, True) - # Get datasets. + # Get datasets and annotations datasets = self.get_history_datasets( trans, history ) - # Get annotations. history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history ) for dataset in datasets: dataset.annotation = self.get_item_annotation_str( trans.sa_session, history.user, dataset ) @@ -957,8 +959,9 @@ else: user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, history ) - return trans.stream_template_mako( "history/display.mako", item = history, item_data = datasets, - user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) + + return trans.stream_template_mako( "history/display.mako", item=history, item_data=datasets, + user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) @web.expose @web.require_login( "share Galaxy histories" ) diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 static/scripts/mvc/history/current-history-panel.js --- /dev/null +++ b/static/scripts/mvc/history/current-history-panel.js @@ -0,0 +1,285 @@ +define([ + "mvc/dataset/hda-edit", + "mvc/history/history-panel" +], function( hdaEdit, hpanel ){ +// ============================================================================ +/** session storage for history panel preferences (and to maintain state) + */ +var HistoryPanelPrefs = SessionStorageModel.extend({ + defaults : { + /** is the panel currently showing the search/filter controls? */ + searching : false, + /** should the tags editor be shown or hidden initially? */ + tagsEditorShown : false, + /** should the annotation editor be shown or hidden initially? */ + annotationEditorShown : false + }, + toString : function(){ + return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')'; + } +}); + +/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */ +HistoryPanelPrefs.storageKey = function storageKey(){ + return ( 'history-panel' ); +}; + +/* ============================================================================= +TODO: + +============================================================================= */ +/** @class View/Controller for the user's current history model as used in the history + * panel (current right hand panel). + * @name HistoryPanel + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var CurrentHistoryPanel = hpanel.HistoryPanel.extend( +/** @lends HistoryPanel.prototype */{ + + ///** logger used to record this.log messages, commonly set to console */ + //// comment this out to suppress log output + //logger : console, + + /** class to use for constructing the HDA views */ + HDAViewClass : hdaEdit.HDAEditView, + + emptyMsg : _l( "This history is empty. Click 'Get Data' on the left pane to start" ), + noneFoundMsg : _l( "No matching datasets found" ), + + // ......................................................................... SET UP + /** Set up the view, set up storage, bind listeners to HDACollection events + * @param {Object} attributes + * @config {Object} urlTemplates.hda nested object containing url templates for HDAViews + * @throws 'needs urlTemplates' if urlTemplates.history or urlTemplates.hda aren't present + * @see PersistentStorage + * @see Backbone.View#initialize + */ + initialize : function( attributes ){ + attributes = attributes || {}; + + // ---- persistent preferences + /** maintain state / preferences over page loads */ + this.preferences = new HistoryPanelPrefs( _.extend({ + id : HistoryPanelPrefs.storageKey() + }, _.pick( attributes, _.keys( HistoryPanelPrefs.prototype.defaults ) ))); + + hpanel.HistoryPanel.prototype.initialize.call( this, attributes ); + if( this.model ){ + console.debug( this.model ); + this.model.checkForUpdates(); + } + }, + + // ------------------------------------------------------------------------ loading history/hda models + /** (re-)loads the user's current history & hdas w/ details */ + loadCurrentHistory : function( attributes ){ + // implemented as a 'fresh start' or for when there is no model (intial panel render) + var panel = this; + return this.loadHistoryWithHDADetails( 'current', attributes ) + .then(function( historyData, hdaData ){ + panel.trigger( 'current-history', panel ); + }); + }, + + /** loads a history & hdas w/ details and makes them the current history */ + switchToHistory : function( historyId, attributes ){ + //console.info( 'switchToHistory:', historyId, attributes ); + var panel = this, + historyFn = function(){ + // make this current and get history data with one call + return jQuery.post( galaxy_config.root + 'api/histories/' + historyId + '/set_as_current' ); + }; + return this.loadHistoryWithHDADetails( historyId, attributes, historyFn ) + .then(function( historyData, hdaData ){ + panel.trigger( 'switched-history', panel ); + }); + }, + + /** creates a new history on the server and sets it as the user's current history */ + createNewHistory : function( attributes ){ + if( !Galaxy || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){ + this.displayMessage( 'error', _l( 'You must be logged in to create histories' ) ); + return $.when(); + } + var panel = this, + historyFn = function(){ + // get history data from posting a new history (and setting it to current) + return jQuery.post( galaxy_config.root + 'api/histories', { current: true }); + }; + // id undefined bc there is no historyId yet - the server will provide + // (no need for details - nothing expanded in new history) + return this.loadHistory( undefined, attributes, historyFn ) + .then(function( historyData, hdaData ){ + panel.trigger( 'new-history', panel ); + }); + }, + + /** release/free/shutdown old models and set up panel for new models */ + setModel : function( newHistoryJSON, newHdaJSON, attributes ){ + attributes = attributes || {}; + hpanel.HistoryPanel.prototype.setModel.call( this, newHistoryJSON, newHdaJSON, attributes ); + this.model.checkForUpdates(); + return this; + }, + + // ------------------------------------------------------------------------ history/hda event listening + /** listening for history and HDA events */ + _setUpModelEventHandlers : function(){ + hpanel.HistoryPanel.prototype._setUpModelEventHandlers.call( this ); + // ---- history + // update the quota meter when current history changes size + if( Galaxy && Galaxy.quotaMeter ){ + this.listenTo( this.model, 'change:nice_size', function(){ + //console.info( '!! model size changed:', this.model.get( 'nice_size' ) ) +//TODO: global + Galaxy.quotaMeter.update(); + }); + } + + // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state, + // then: remove it from the collection if the panel is set to NOT show hidden datasets + this.model.hdas.on( 'state:ready', function( hda, newState, oldState ){ + if( ( !hda.get( 'visible' ) ) + && ( !this.storage.get( 'show_hidden' ) ) ){ + this.removeHdaView( this.hdaViews[ hda.id ] ); + } + }, this ); + + }, + + // ------------------------------------------------------------------------ panel rendering + /** Render urls, historyPanel body, and hdas (if any are shown) + * @fires: rendered when the panel is attached and fully visible + * @see Backbone.View#render + */ + render : function( speed, callback ){ + // send a speed of 0 to have no fade in/out performed + speed = ( speed === undefined )?( this.fxSpeed ):( speed ); + var panel = this, + $newRender; + + // handle the possibility of no model (can occur if fetching the model returns an error) + if( this.model ){ + $newRender = this.renderModel(); + } else { + $newRender = this.renderWithoutModel(); + } + + // fade out existing, swap with the new, fade in, set up behaviours + $( panel ).queue( 'fx', [ + function( next ){ + //panel.$el.fadeTo( panel.fxSpeed, 0.0001, next ); + if( speed && panel.$el.is( ':visible' ) ){ + panel.$el.fadeOut( speed, next ); + } else { + next(); + } + }, + function( next ){ + // swap over from temp div newRender + panel.$el.empty(); + if( $newRender ){ + panel.$el.append( $newRender.children() ); + panel.renderBasedOnPrefs(); + } + next(); + }, + function( next ){ + if( speed && !panel.$el.is( ':visible' ) ){ + panel.$el.fadeIn( speed, next ); + } else { + next(); + } + }, + function( next ){ + //TODO: ideally, these would be set up before the fade in (can't because of async save text) + if( callback ){ callback.call( this ); } + panel.trigger( 'rendered', this ); + next(); + } + ]); + return this; + }, + + renderBasedOnPrefs : function(){ + if( this.preferences.get( 'searching' ) ){ + this.showSearchControls( 0 ); + } + }, + + // ........................................................................ external objects/MVC + //TODO: remove quota meter from panel and remove this + /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */ + connectToQuotaMeter : function( quotaMeter ){ + if( !quotaMeter ){ + return this; + } + // show/hide the 'over quota message' in the history when the meter tells it to + this.listenTo( quotaMeter, 'quota:over', this.showQuotaMessage ); + this.listenTo( quotaMeter, 'quota:under', this.hideQuotaMessage ); + + // having to add this to handle re-render of hview while overquota (the above do not fire) + this.on( 'rendered rendered:initial', function(){ + if( quotaMeter && quotaMeter.isOverQuota() ){ + this.showQuotaMessage(); + } + }); + return this; + }, + +//TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here + /** Show the over quota message (which happens to be in the history panel). + */ + showQuotaMessage : function(){ + var msg = this.$el.find( '.quota-message' ); + //this.log( this + ' showing quota message:', msg, userData ); + if( msg.is( ':hidden' ) ){ msg.slideDown( this.fxSpeed ); } + }, + +//TODO: this seems more like a per user message than a history message + /** Hide the over quota message (which happens to be in the history panel). + */ + hideQuotaMessage : function(){ + var msg = this.$el.find( '.quota-message' ); + //this.log( this + ' hiding quota message:', msg, userData ); + if( !msg.is( ':hidden' ) ){ msg.slideUp( this.fxSpeed ); } + }, + +//TODO: move show_deleted/hidden into panel from opt menu and remove this + /** add listeners to an external options menu (templates/webapps/galaxy/root/index.mako) */ + connectToOptionsMenu : function( optionsMenu ){ + if( !optionsMenu ){ + return this; + } + // set a visible indication in the popupmenu for show_hidden/deleted based on the currHistoryPanel's settings + this.on( 'new-storage', function( storage, panel ){ + if( optionsMenu && storage ){ + optionsMenu.findItemByHtml( _l( 'Include Deleted Datasets' ) ).checked = storage.get( 'show_deleted' ); + optionsMenu.findItemByHtml( _l( 'Include Hidden Datasets' ) ).checked = storage.get( 'show_hidden' ); + } + }); + return this; + }, + + /** Return a string rep of the history + */ + toString : function(){ + return 'CurrentHistoryPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; + } +}); + +//------------------------------------------------------------------------------ TEMPLATES +CurrentHistoryPanel.templates = { + historyPanel : Handlebars.templates[ 'template-history-historyPanel' ], + anonHistoryPanel : Handlebars.templates[ 'template-history-historyPanel-anon' ] +}; + +//============================================================================== + return { + CurrentHistoryPanel : CurrentHistoryPanel + }; +}); diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -75,7 +75,7 @@ /** cached timeout id for the HDA updater */ this.updateTimeoutId = null; // set up update timeout if needed - this.checkForUpdates(); + //this.checkForUpdates(); }, /** set up any event listeners for this history including those to the contained HDAs diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -1,157 +1,46 @@ define([ - "mvc/history/history-model", "mvc/dataset/hda-model", - "mvc/dataset/hda-base", - "mvc/dataset/hda-edit" -], function( historyModel, hdaModel, hdaBase, hdaEdit ){ + "mvc/dataset/hda-edit", + "mvc/history/readonly-history-panel" +], function( hdaModel, hdaEdit, readonlyPanel ){ +/* ============================================================================= +TODO: - -// ============================================================================ -/** session storage for history panel preferences (and to maintain state) - */ -var HistoryPanelPrefs = SessionStorageModel.extend({ - defaults : { - /** is the panel currently showing the search/filter controls? */ - searching : false, - /** should the tags editor be shown or hidden initially? */ - tagsEditorShown : false, - /** should the annotation editor be shown or hidden initially? */ - annotationEditorShown : false - }, - toString : function(){ - return 'HistoryPanelPrefs(' + JSON.stringify( this.toJSON() ) + ')'; - } -}); - -/** key string to store panel prefs (made accessible on class so you can access sessionStorage directly) */ -HistoryPanelPrefs.storageKey = function storageKey(){ - return ( 'history-panel' ); -}; - - -// ============================================================================ -/** session storage for individual history preferences - */ -var HistoryPrefs = SessionStorageModel.extend({ - defaults : { - //TODO:?? expandedHdas to array? - expandedHdas : {}, - //TODO:?? move to user? - show_deleted : false, - show_hidden : false - //TODO: add scroll position? - }, - /** add an hda id to the hash of expanded hdas */ - addExpandedHda : function( id ){ - this.save( 'expandedHdas', _.extend( this.get( 'expandedHdas' ), _.object([ id ], [ true ]) ) ); - }, - /** remove an hda id from the hash of expanded hdas */ - removeExpandedHda : function( id ){ - this.save( 'expandedHdas', _.omit( this.get( 'expandedHdas' ), id ) ); - }, - toString : function(){ - return 'HistoryPrefs(' + this.id + ')'; - } -}); - -/** key string to store each histories settings under */ -HistoryPrefs.historyStorageKey = function historyStorageKey( historyId ){ - // class lvl for access w/o instantiation - if( !historyId ){ - throw new Error( 'HistoryPrefs.historyStorageKey needs valid id: ' + historyId ); - } - // single point of change - return ( 'history:' + historyId ); -}; - - -/* ============================================================================= -Backbone.js implementation of history panel - -r.js optimizer cline: -r.js -o baseUrl=. name=./mvc/history/history-panel.js out=history-panel.min.js - -TODO: - tags & annotations -> out - use model.save instead of urls - - feature creep: - lineage - hide button - show permissions in info - show shared/sharing status on ds, history - selection, multi-select (and actions common to selected (ugh)) - searching - sorting, re-shuffling - ============================================================================= */ -/** @class View/Controller for the history model as used in the history - * panel (current right hand panel). +/** @class View/Controller for the history model. * @name HistoryPanel * + * Allows: + * (everything ReadOnlyHistoryPanel allows) + * changing the name + * displaying and editing tags and annotations + * multi-selection and operations on mulitple hdas + * Does not allow: + * changing the name + * * @augments Backbone.View * @borrows LoggableMixin#logger as #logger * @borrows LoggableMixin#log as #log * @constructs */ -var HistoryPanel = Backbone.View.extend( LoggableMixin ).extend( +var HistoryPanel = readonlyPanel.ReadOnlyHistoryPanel.extend( /** @lends HistoryPanel.prototype */{ - + ///** logger used to record this.log messages, commonly set to console */ //// comment this out to suppress log output //logger : console, - /** which class to use for constructing the HDA views */ - //defaultHDAViewClass : hdaBase.HDABaseView, - defaultHDAViewClass : hdaEdit.HDAEditView, + /** class to use for constructing the HDA views */ + HDAViewClass : hdaEdit.HDAEditView, - tagName : 'div', - className : 'history-panel', - - /** (in ms) that jquery effects will use */ - fxSpeed : 'fast', - - datasetsSelector : '.datasets-list', - emptyMsgSelector : '.empty-history-message', - msgsSelector : '.message-container', - // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HDACollection events * @param {Object} attributes - * @config {Object} urlTemplates.hda nested object containing url templates for HDAViews - * @throws 'needs urlTemplates' if urlTemplates.history or urlTemplates.hda aren't present - * @see PersistentStorage - * @see Backbone.View#initialize */ initialize : function( attributes ){ attributes = attributes || {}; - // set the logger if requested - if( attributes.logger ){ - this.logger = attributes.logger; - } - this.log( this + '.initialize:', attributes ); // ---- set up instance vars - // control contents/behavior based on where (and in what context) the panel is being used - /** which backbone view class to use when displaying the hda list */ - this.HDAViewClass = attributes.HDAViewClass || this.defaultHDAViewClass; - /** where should pages from links be displayed? (default to new tab/window) */ - this.linkTarget = attributes.linkTarget || '_blank'; - - // ---- sub views and saved elements - /** map of hda model ids to hda views */ - this.hdaViews = {}; - /** loading indicator */ - this.indicator = new LoadingIndicator( this.$el ); - - // ---- persistent state and preferences - /** maintain state / preferences over page loads */ - this.preferences = new HistoryPanelPrefs( _.extend({ - id : HistoryPanelPrefs.storageKey() - }, _.pick( attributes, _.keys( HistoryPanelPrefs.prototype.defaults ) ))); - - /** filters for displaying hdas */ - this.filters = []; /** selected hda ids */ this.selectedHdaIds = []; @@ -161,443 +50,33 @@ this.annotationEditorShown = attributes.annotationEditorShown || false; this.tagsEditorShown = attributes.tagsEditorShown || false; - this._setUpListeners(); - - // ---- handle models passed on init - if( this.model ){ - this._setUpWebStorage( attributes.initiallyExpanded, attributes.show_deleted, attributes.show_hidden ); - this._setUpModelEventHandlers(); - } -//TODO: remove? - // ---- and any run functions - if( attributes.onready ){ - attributes.onready.call( this ); - } + readonlyPanel.ReadOnlyHistoryPanel.prototype.initialize.call( this, attributes ); }, - /** create any event listeners for the panel - * @fires: rendered:initial on the first render - * @fires: empty-history when switching to a history with no HDAs or creating a new history - */ - _setUpListeners : function(){ - // ---- event handlers for self - this.on( 'error', function( model, xhr, options, msg, details ){ - this.errorHandler( model, xhr, options, msg, details ); - }); - - this.on( 'loading-history', function(){ - // show the loading indicator when loading a new history starts... - this.showLoadingIndicator( 'loading history...', 40 ); - }); - this.on( 'loading-done', function(){ - // ...hiding it again when loading is done (or there's been an error) - this.hideLoadingIndicator( 40 ); - }); - - // throw the first render up as a diff namespace using once - // (for outside consumption) - this.once( 'rendered', function(){ - this.trigger( 'rendered:initial', this ); - return false; - }); - - // trigger an event when there are no visible hdas - // (for outside consumption) - this.on( 'switched-history current-history new-history', function(){ - if( _.isEmpty( this.hdaViews ) ){ - this.trigger( 'empty-history', this ); - } - }); - - // debugging - if( this.logger ){ - this.on( 'all', function( event ){ - this.log( this + '', arguments ); - }, this ); - } - }, - - //TODO: see base-mvc - //onFree : function(){ - // _.each( this.hdaViews, function( view, modelId ){ - // view.free(); - // }); - // this.hdaViews = null; - //}, - - // ........................................................................ error handling - /** Event listener to handle errors (from the panel, the history, or the history's HDAs) - * @param {Model or View} model the (Backbone) source of the error - * @param {XMLHTTPRequest} xhr any ajax obj. assoc. with the error - * @param {Object} options the options map commonly used with bbone ajax - * @param {String} msg optional message passed to ease error location - * @param {Object} msg optional object containing error details - */ - errorHandler : function( model, xhr, options, msg, details ){ - var parsed = this._parseErrorMessage( model, xhr, options, msg, details ); - - // interrupted ajax - if( xhr && xhr.status === 0 && xhr.readyState === 0 ){ - - // bad gateway - } else if( xhr && xhr.status === 502 ){ -//TODO: gmail style 'reconnecting in Ns' - - // otherwise, show an error message inside the panel - } else { - // it's possible to have a triggered error before the message container is rendered - wait for it to show - if( !this.$el.find( this.msgsSelector ).is( ':visible' ) ){ - this.once( 'rendered', function(){ - this.displayMessage( 'error', parsed.message, parsed.details ); - }); - } else { - this.displayMessage( 'error', parsed.message, parsed.details ); - } - } - }, - - /** Parse an error event into an Object usable by displayMessage based on the parameters - * note: see errorHandler for more info on params - */ - _parseErrorMessage : function( model, xhr, options, msg, details ){ - var user = Galaxy.currUser, - // add the args (w/ some extra info) into an obj - parsed = { - message : this._bePolite( msg ), - details : { - user : ( user instanceof User )?( user.toJSON() ):( user + '' ), - source : ( model instanceof Backbone.Model )?( model.toJSON() ):( model + '' ), - xhr : xhr, - options : ( xhr )?( _.omit( options, 'xhr' ) ):( options ) - } - }; - // add any extra details passed in - _.extend( parsed.details, details || {} ); - // fancy xhr.header parsing (--> obj) - if( xhr && _.isFunction( xhr.getAllResponseHeaders ) ){ - var responseHeaders = xhr.getAllResponseHeaders(); - responseHeaders = _.compact( responseHeaders.split( '\n' ) ); - responseHeaders = _.map( responseHeaders, function( header ){ - return header.split( ': ' ); - }); - parsed.details.xhr.responseHeaders = _.object( responseHeaders ); - } - return parsed; - }, - - /** Modify an error message to be fancy and wear a monocle. */ - _bePolite : function( msg ){ - msg = msg || _l( 'An error occurred while getting updates from the server' ); - return msg + '. ' + _l( 'Please contact a Galaxy administrator if the problem persists.' ); - }, - - // ------------------------------------------------------------------------ loading history/hda models - - //NOTE: all the following fns replace the existing history model with a new model - // (in the following 'details' refers to the full set of hda api data (urls, display_apps, misc_info, etc.) - // - hdas w/o details will have summary data only (name, hid, deleted, visible, state, etc.)) - - /** (re-)loads the user's current history & hdas w/ details */ - loadCurrentHistory : function( attributes ){ - // implemented as a 'fresh start' or for when there is no model (intial panel render) - var panel = this; - return this.loadHistoryWithHDADetails( 'current', attributes ) - .then(function( historyData, hdaData ){ - panel.trigger( 'current-history', panel ); - }); - }, - - /** loads a history & hdas w/ details and makes them the current history */ - switchToHistory : function( historyId, attributes ){ - //console.info( 'switchToHistory:', historyId, attributes ); - var panel = this, - historyFn = function(){ - // make this current and get history data with one call - return jQuery.post( galaxy_config.root + 'api/histories/' + historyId + '/set_as_current' ); - }; - return this.loadHistoryWithHDADetails( historyId, attributes, historyFn ) - .then(function( historyData, hdaData ){ - panel.trigger( 'switched-history', panel ); - }); - }, - - /** creates a new history on the server and sets it as the user's current history */ - createNewHistory : function( attributes ){ - if( !Galaxy || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){ - this.displayMessage( 'error', _l( 'You must be logged in to create histories' ) ); - return $.when(); - } - var panel = this, - historyFn = function(){ - // get history data from posting a new history (and setting it to current) - return jQuery.post( galaxy_config.root + 'api/histories', { current: true }); - }; - // id undefined bc there is no historyId yet - the server will provide - // (no need for details - nothing expanded in new history) - return this.loadHistory( undefined, attributes, historyFn ) - .then(function( historyData, hdaData ){ - panel.trigger( 'new-history', panel ); - }); - }, - - /** loads a history & hdas w/ details (but does not make them the current history) */ - loadHistoryWithHDADetails : function( historyId, attributes, historyFn, hdaFn ){ - //console.info( 'loadHistoryWithHDADetails:', historyId, attributes, historyFn, hdaFn ); - var panel = this, - // will be called to get hda ids that need details from the api - hdaDetailIds = function( historyData ){ -//TODO: non-visible HDAs are getting details loaded... either stop loading them at all or filter ids thru isVisible - return panel.getExpandedHdaIds( historyData.id ); - }; - return this.loadHistory( historyId, attributes, historyFn, hdaFn, hdaDetailIds ); - }, - - /** loads a history & hdas w/ NO details (but does not make them the current history) */ - loadHistory : function( historyId, attributes, historyFn, hdaFn, hdaDetailIds ){ - this.trigger( 'loading-history', this ); - attributes = attributes || {}; - var panel = this; - //console.info( 'loadHistory:', historyId, attributes, historyFn, hdaFn, hdaDetailIds ); - var xhr = historyModel.History.getHistoryData( historyId, { - historyFn : historyFn, - hdaFn : hdaFn, - hdaDetailIds : attributes.initiallyExpanded || hdaDetailIds - }); - return this._loadHistoryFromXHR( xhr, attributes ) - .fail( function( xhr, where, history ){ - // throw an error up for the error handler - panel.trigger( 'error', panel, xhr, attributes, _l( 'An error was encountered while ' + where ), - { historyId: historyId, history: history || {} }); - }) - .always( function(){ - // bc hideLoadingIndicator relies on this firing - panel.trigger( 'loading-done', panel ); - }); - }, - - /** given an xhr that will provide both history and hda data, pass data to set model or handle xhr errors */ - _loadHistoryFromXHR : function( xhr, attributes ){ - var panel = this; - xhr.then( function( historyJSON, hdaJSON ){ - panel.setModel( historyJSON, hdaJSON, attributes ); - }); - xhr.fail( function( xhr, where ){ - // always render - whether we get a model or not - panel.render(); - }); - return xhr; - }, - - /** release/free/shutdown old models and set up panel for new models */ - setModel : function( newHistoryJSON, newHdaJSON, attributes ){ - attributes = attributes || {}; - //console.info( 'setModel:', newHistoryJSON, newHdaJSON.length, attributes ); - - // stop/release the previous model, and clear cache to hda sub-views - if( this.model ){ - this.model.clearUpdateTimeout(); - this.stopListening( this.model ); - this.stopListening( this.model.hdas ); - //TODO: see base-mvc - //this.model.free(); - } - this.hdaViews = {}; - - // set up the new model and render - if( Galaxy && Galaxy.currUser ){ -//TODO: global - newHistoryJSON.user = Galaxy.currUser.toJSON(); - } - this.model = new historyModel.History( newHistoryJSON, newHdaJSON, attributes ); - this._setUpWebStorage( attributes.initiallyExpanded, attributes.show_deleted, attributes.show_hidden ); - this._setUpModelEventHandlers(); - this.selectedHdaIds = []; - this.trigger( 'new-model', this ); - this.render(); - return this; - }, - - // ------------------------------------------------------------------------ browser stored prefs - /** Set up client side storage. Currently PersistanStorage keyed under 'HistoryPanel.<id>' - * @param {Object} initiallyExpanded - * @param {Boolean} show_deleted whether to show deleted HDAs (overrides stored) - * @param {Boolean} show_hidden - * @see PersistentStorage - */ - _setUpWebStorage : function( initiallyExpanded, show_deleted, show_hidden ){ - //console.debug( '_setUpWebStorage', initiallyExpanded, show_deleted, show_hidden ); - this.storage = new HistoryPrefs({ - id: HistoryPrefs.historyStorageKey( this.model.get( 'id' ) ) - }); - - // expanded Hdas is a map of hda.ids -> a boolean repr'ing whether this hda's body is already expanded - // store any pre-expanded ids passed in - if( _.isObject( initiallyExpanded ) ){ - this.storage.set( 'exandedHdas', initiallyExpanded ); - } - - // get the show_deleted/hidden settings giving priority to values passed in, using web storage otherwise - // if the page has specifically requested show_deleted/hidden, these will be either true or false - // (as opposed to undefined, null) - and we give priority to that setting - if( _.isBoolean( show_deleted ) ){ - this.storage.set( 'show_deleted', show_deleted ); - } - if( _.isBoolean( show_hidden ) ){ - this.storage.set( 'show_hidden', show_hidden ); - } - - this.trigger( 'new-storage', this.storage, this ); - this.log( this + ' (init\'d) storage:', this.storage.get() ); - }, - - /** clear all stored history panel data */ - clearWebStorage : function(){ - for( var key in sessionStorage ){ - if( key.indexOf( 'history:' ) === 0 ){ - sessionStorage.removeItem( key ); - } - } - }, - - /** get all stored data as an Object for a history with the given id */ - getStoredOptions : function( historyId ){ - if( !historyId || historyId === 'current' ){ - return ( this.storage )?( this.storage.get() ):( {} ); - } - //TODO: make storage engine generic - var item = sessionStorage.getItem( HistoryPrefs.historyStorageKey( historyId ) ); - return ( item === null )?( {} ):( JSON.parse( item ) ); - }, - - /** get an array of expanded hda ids for the given history id */ - getExpandedHdaIds : function( historyId ){ - var expandedHdas = this.getStoredOptions( historyId ).expandedHdas; - return (( _.isEmpty( expandedHdas ) )?( [] ):( _.keys( expandedHdas ) )); - }, - - // ------------------------------------------------------------------------ history/hda event listening + // ------------------------------------------------------------------------ panel rendering /** listening for history and HDA events */ _setUpModelEventHandlers : function(){ - // ---- history - // on a model error - bounce it up to the panel and remove it from the model - this.model.on( 'error error:hdas', function( model, xhr, options, msg ){ - this.errorHandler( model, xhr, options, msg ); - }, this ); + readonlyPanel.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call( this ); - // don't need to re-render entire model on all changes, just render disk size when it changes this.model.on( 'change:nice_size', this.updateHistoryDiskSize, this ); - // update the quota meter when current history changes size - if( Galaxy && Galaxy.quotaMeter ){ - this.listenTo( this.model, 'change:nice_size', function(){ - //console.info( '!! model size changed:', this.model.get( 'nice_size' ) ) -//TODO: global - Galaxy.quotaMeter.update(); - }); - } - - // ---- hdas - // bind events from the model's hda collection - // note: don't listen to the hdas for errors, history will pass that to us - //this.model.hdas.on( 'reset', this.addAll, this ); - this.model.hdas.on( 'add', this.addHdaView, this ); - this.model.hdas.on( 'change:deleted', this.handleHdaDeletionChange, this ); this.model.hdas.on( 'change:visible', this.handleHdaVisibleChange, this ); - // when an hda is purged the disk size changes this.model.hdas.on( 'change:purged', function( hda ){ // hafta get the new nice-size w/o the purged hda this.model.fetch(); }, this ); - - // if an a hidden hda is created (gen. by a workflow), moves thru the updater to the ready state, - // then: remove it from the collection if the panel is set to NOT show hidden datasets - this.model.hdas.on( 'state:ready', function( hda, newState, oldState ){ - if( ( !hda.get( 'visible' ) ) - && ( !this.storage.get( 'show_hidden' ) ) ){ - this.removeHdaView( this.hdaViews[ hda.id ] ); - } - }, this ); - }, // ------------------------------------------------------------------------ panel rendering - /** Render urls, historyPanel body, and hdas (if any are shown) - * @fires: rendered when the panel is attached and fully visible - * @see Backbone.View#render - */ - render : function( speed, callback ){ - // send a speed of 0 to have no fade in/out performed - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var panel = this, - $newRender; - - // handle the possibility of no model (can occur if fetching the model returns an error) - if( this.model ){ - $newRender = this.renderModel(); - } else { - $newRender = this.renderWithoutModel(); - } - - // fade out existing, swap with the new, fade in, set up behaviours - $( panel ).queue( 'fx', [ - function( next ){ - //panel.$el.fadeTo( panel.fxSpeed, 0.0001, next ); - if( speed && panel.$el.is( ':visible' ) ){ - panel.$el.fadeOut( speed, next ); - } else { - next(); - } - }, - function( next ){ - // swap over from temp div newRender - panel.$el.empty(); - if( $newRender ){ - panel.$el.append( $newRender.children() ); - panel.renderBasedOnPrefs(); - } - next(); - }, - function( next ){ - if( speed && !panel.$el.is( ':visible' ) ){ - panel.$el.fadeIn( speed, next ); - } else { - next(); - } - }, - function( next ){ - //TODO: ideally, these would be set up before the fade in (can't because of async save text) - if( callback ){ callback.call( this ); } - panel.trigger( 'rendered', this ); - next(); - } - ]); - return this; - }, - - /** render with no history data */ - renderWithoutModel : function( ){ - // we'll always need the message container - var $newRender = $( '<div/>' ), - $msgContainer = $( '<div/>' ).addClass( 'message-container' ) - .css({ 'margin-left': '4px', 'margin-right': '4px' }); - return $newRender.append( $msgContainer ); - }, - /** render with history data */ renderModel : function( ){ var $newRender = $( '<div/>' ); - // render based on anonymity, set up behaviors - if( !Galaxy || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){ - $newRender.append( HistoryPanel.templates.anonHistoryPanel( this.model.toJSON() ) ); - - } else { - $newRender.append( HistoryPanel.templates.historyPanel( this.model.toJSON() ) ); - if( Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){ - this._renderTags( $newRender ); - this._renderAnnotation( $newRender ); - } + $newRender.append( HistoryPanel.templates.historyPanel( this.model.toJSON() ) ); + if( Galaxy.currUser.id && Galaxy.currUser.id === this.model.get( 'user_id' ) ){ + this._renderTags( $newRender ); + this._renderAnnotation( $newRender ); } // search and select available to both anon/logged-in users $newRender.find( '.history-secondary-actions' ).prepend( this._renderSelectButton() ); @@ -611,12 +90,6 @@ return $newRender; }, - renderBasedOnPrefs : function(){ - if( this.preferences.get( 'searching' ) ){ - this.showSearchControls( 0 ); - } - }, - _renderTags : function( $where ){ var panel = this; this.tagsEditor = new TagsEditor({ @@ -625,11 +98,9 @@ onshowFirstTime : function(){ this.render(); }, // show hide hda view tag editors when this is shown/hidden onshow : function(){ - panel.preferences.set( 'tagsEditorShown', true ); panel.toggleHDATagEditors( true, panel.fxSpeed ); }, onhide : function(){ - panel.preferences.set( 'tagsEditorShown', false ); panel.toggleHDATagEditors( false, panel.fxSpeed ); }, $activator : faIconButton({ @@ -638,9 +109,6 @@ faIcon : 'fa-tags' }).appendTo( $where.find( '.history-secondary-actions' ) ) }); - if( this.preferences.get( 'tagsEditorShown' ) ){ - this.tagsEditor.toggle( true ); - } }, _renderAnnotation : function( $where ){ var panel = this; @@ -650,11 +118,9 @@ onshowFirstTime : function(){ this.render(); }, // show hide hda view annotation editors when this is shown/hidden onshow : function(){ - panel.preferences.set( 'annotationEditorShown', true ); panel.toggleHDAAnnotationEditors( true, panel.fxSpeed ); }, onhide : function(){ - panel.preferences.set( 'annotationEditorShown', false ); panel.toggleHDAAnnotationEditors( false, panel.fxSpeed ); }, $activator : faIconButton({ @@ -663,18 +129,8 @@ faIcon : 'fa-comment' }).appendTo( $where.find( '.history-secondary-actions' ) ) }); - if( this.preferences.get( 'annotationEditorShown' ) ){ - this.annotationEditor.toggle( true ); - } }, - /** button for opening search */ - _renderSearchButton : function( $where ){ - return faIconButton({ - title : _l( 'Search datasets' ), - classes : 'history-search-btn', - faIcon : 'fa-search' - }); - }, + /** button for starting select mode */ _renderSelectButton : function( $where ){ return faIconButton({ @@ -762,45 +218,23 @@ }, // ------------------------------------------------------------------------ hda sub-views - /** alias to the model. Updates the hda list only (not the history) */ - refreshHdas : function( detailIds, options ){ - if( this.model ){ - return this.model.refresh( detailIds, options ); - } - // may have callbacks - so return an empty promise - return $.when(); + /** If this hda is deleted and we're not showing deleted hdas, remove the view + * @param {HistoryDataAssociation} the hda to check + */ + handleHdaDeletionChange : function( hda ){ + if( hda.get( 'deleted' ) && !this.storage.get( 'show_deleted' ) ){ + this.removeHdaView( this.hdaViews[ hda.id ] ); + } // otherwise, the hdaView rendering should handle it }, - /** Add an hda view to the panel for the given hda - * @param {HistoryDatasetAssociation} hda + + /** If this hda is hidden and we're not showing hidden hdas, remove the view + * @param {HistoryDataAssociation} the hda to check */ - addHdaView : function( hda ){ - this.log( 'add.' + this, hda ); - var panel = this; - - // don't add the view if it wouldn't be visible accrd. to current settings - if( !hda.isVisible( this.storage.get( 'show_deleted' ), this.storage.get( 'show_hidden' ) ) ){ - return; - } - - // create and prepend to current el, if it was empty fadeout the emptyMsg first - $({}).queue([ - function fadeOutEmptyMsg( next ){ - var $emptyMsg = panel.$el.find( panel.emptyMsgSelector ); - if( $emptyMsg.is( ':visible' ) ){ - $emptyMsg.fadeOut( panel.fxSpeed, next ); - } else { - next(); - } - }, - function createAndPrepend( next ){ - panel.scrollToTop(); - var $whereTo = panel.$el.find( panel.datasetsSelector ), - hdaView = panel.createHdaView( hda ); - panel.hdaViews[ hda.id ] = hdaView; - hdaView.render().$el.hide().prependTo( $whereTo ).slideDown( panel.fxSpeed ); - } - ]); + handleHdaVisibleChange : function( hda ){ + if( hda.hidden() && !this.storage.get( 'show_hidden' ) ){ + this.removeHdaView( this.hdaViews[ hda.id ] ); + } // otherwise, the hdaView rendering should handle it }, /** Create an HDA view for the given HDA (but leave attachment for addHdaView above) @@ -816,8 +250,8 @@ selectable : this.selecting, hasUser : this.model.ownedByCurrUser(), logger : this.logger, - tagsEditorShown : this.preferences.get( 'tagsEditorShown' ), - annotationEditorShown : this.preferences.get( 'annotationEditorShown' ) + tagsEditorShown : !this.tagsEditor.isHidden(), + annotationEditorShown : !this.annotationEditor.isHidden() }); this._setUpHdaListeners( hdaView ); return hdaView; @@ -829,13 +263,8 @@ */ _setUpHdaListeners : function( hdaView ){ var historyView = this; - // maintain a list of hdas whose bodies are expanded - hdaView.on( 'body-expanded', function( id ){ - historyView.storage.addExpandedHda( id ); - }); - hdaView.on( 'body-collapsed', function( id ){ - historyView.storage.removeExpandedHda( id ); - }); + readonlyPanel.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call( this, hdaView ); + // maintain a list of hdas that are selected hdaView.on( 'selected', function( hdaView ){ var id = hdaView.model.get( 'id' ); @@ -847,88 +276,6 @@ historyView.selectedHdaIds = _.without( historyView.selectedHdaIds, id ); //console.debug( 'de-selected', historyView.selectedHdaIds ); }); -//TODO: remove? - hdaView.on( 'error', function( model, xhr, options, msg ){ - historyView.errorHandler( model, xhr, options, msg ); - }); - }, - - /** If this hda is deleted and we're not showing deleted hdas, remove the view - * @param {HistoryDataAssociation} the hda to check - */ - handleHdaDeletionChange : function( hda ){ - if( hda.get( 'deleted' ) && !this.storage.get( 'show_deleted' ) ){ - this.removeHdaView( this.hdaViews[ hda.id ] ); - } // otherwise, the hdaView rendering should handle it - }, - - /** If this hda is hidden and we're not showing hidden hdas, remove the view - * @param {HistoryDataAssociation} the hda to check - */ - handleHdaVisibleChange : function( hda ){ - if( hda.hidden() && !this.storage.get( 'show_hidden' ) ){ - this.removeHdaView( this.hdaViews[ hda.id ] ); - } // otherwise, the hdaView rendering should handle it - }, - - /** Remove a view from the panel and if the panel is now empty, re-render - * @param {Int} the id of the hdaView to remove - */ - removeHdaView : function( hdaView ){ - if( !hdaView ){ return; } - - var panel = this; - hdaView.$el.fadeOut( panel.fxSpeed, function(){ - hdaView.off(); - hdaView.remove(); - delete panel.hdaViews[ hdaView.model.id ]; - if( _.isEmpty( panel.hdaViews ) ){ - panel.$el.find( panel.emptyMsgSelector ).fadeIn( panel.fxSpeed, function(){ - panel.trigger( 'empty-history', panel ); - }); - } - }); - }, - - /** Set up/render a view for each HDA to be shown, init with model and listeners. - * HDA views are cached to the map this.hdaViews (using the model.id as key). - * @param {jQuery} $whereTo what dom element to prepend the HDA views to - * @returns the number of visible hda views - */ - renderHdas : function( $whereTo ){ - $whereTo = $whereTo || this.$el; - var historyView = this, - newHdaViews = {}, - $datasetsList = $whereTo.find( this.datasetsSelector ), - // only render the shown hdas - //TODO: switch to more general filtered pattern - visibleHdas = this.model.hdas.getVisible( - this.storage.get( 'show_deleted' ), - this.storage.get( 'show_hidden' ), - this.filters - ); - //console.debug( 'renderHdas, visibleHdas:', visibleHdas, $whereTo ); - $datasetsList.empty(); - - if( visibleHdas.length ){ - visibleHdas.each( function( hda ){ - // render it (NOTE: reverse order, newest on top (prepend)) - var hdaId = hda.get( 'id' ), - hdaView = historyView.createHdaView( hda ); - newHdaViews[ hdaId ] = hdaView; - if( _.contains( historyView.selectedHdaIds, hdaId ) ){ - hdaView.selected = true; - } - $datasetsList.prepend( hdaView.render().$el ); - }); - $whereTo.find( this.emptyMsgSelector ).hide(); - - } else { - //console.debug( 'emptyMsg:', $whereTo.find( this.emptyMsgSelector ) ) - $whereTo.find( this.emptyMsgSelector ).show(); - } - this.hdaViews = newHdaViews; - return this.hdaViews; }, /** toggle the visibility of each hdaView's tagsEditor applying all the args sent to this function */ @@ -951,149 +298,41 @@ }); }, + /** Remove a view from the panel and if the panel is now empty, re-render + * @param {Int} the id of the hdaView to remove + */ + removeHdaView : function( hdaView ){ + if( !hdaView ){ return; } + + var panel = this; + hdaView.$el.fadeOut( panel.fxSpeed, function(){ + hdaView.off(); + hdaView.remove(); + delete panel.hdaViews[ hdaView.model.id ]; + if( _.isEmpty( panel.hdaViews ) ){ + panel.$el.find( panel.emptyMsgSelector ).fadeIn( panel.fxSpeed, function(){ + panel.trigger( 'empty-history', panel ); + }); + } + }); + }, + // ------------------------------------------------------------------------ panel events /** event map */ - events : { - // allow (error) messages to be clicked away - //TODO: switch to common close (X) idiom - 'click .message-container' : 'clearMessages', - - 'click .history-search-btn' : 'toggleSearchControls', + events : _.extend( _.clone( readonlyPanel.ReadOnlyHistoryPanel.prototype.events ), { 'click .history-select-btn' : function( e ){ this.toggleSelectors( this.fxSpeed ); }, - 'click .history-select-all-datasets-btn' : 'selectAllDatasets', 'click .history-deselect-all-datasets-btn' : 'deselectAllDatasets' - }, + }), /** Update the history size display (curr. upper right of panel). */ updateHistoryDiskSize : function(){ this.$el.find( '.history-size' ).text( this.model.get( 'nice_size' ) ); }, - - /** Collapse all hda bodies and clear expandedHdas in the storage - */ - collapseAllHdaBodies : function(){ - _.each( this.hdaViews, function( item ){ - item.toggleBodyVisibility( null, false ); - }); - this.storage.set( 'expandedHdas', {} ); - }, - - /** Handle the user toggling the deleted visibility by: - * (1) storing the new value in the persistent storage - * (2) re-rendering the history - * @returns {Boolean} new show_deleted setting - */ - toggleShowDeleted : function(){ - this.storage.set( 'show_deleted', !this.storage.get( 'show_deleted' ) ); - this.renderHdas(); - return this.storage.get( 'show_deleted' ); - }, - - /** Handle the user toggling the deleted visibility by: - * (1) storing the new value in the persistent storage - * (2) re-rendering the history - * @returns {Boolean} new show_hidden setting - */ - toggleShowHidden : function(){ - this.storage.set( 'show_hidden', !this.storage.get( 'show_hidden' ) ); - this.renderHdas(); - return this.storage.get( 'show_hidden' ); - }, - - // ........................................................................ filters - /** render a search input for filtering datasets shown - * (see the search section in the HDA model for implementation of the actual searching) - * return will start the search - * esc will clear the search - * clicking the clear button will clear the search - * uses searchInput in ui.js - */ - setUpSearchInput : function( $where ){ - var panel = this, - inputSelector = '.history-search-input'; - - function onSearch( searchFor ){ - //console.debug( 'onSearch', searchFor, panel ); - panel.searchFor = searchFor; - panel.filters = [ function( hda ){ return hda.matchesAll( panel.searchFor ); } ]; - panel.trigger( 'search:searching', searchFor, panel ); - panel.renderHdas(); - } - function onFirstSearch( searchFor ){ - //console.debug( 'onSearch', searchFor, panel ); - if( panel.model.hdas.haveDetails() ){ - onSearch( searchFor ); - return; - } - panel.$el.find( inputSelector ).searchInput( 'toggle-loading' ); - panel.model.hdas.fetchAllDetails({ silent: true }) - .always( function(){ - panel.$el.find( inputSelector ).searchInput( 'toggle-loading' ); - }) - .done( function(){ - onSearch( searchFor ); - }); - } - function onSearchClear(){ - //console.debug( 'onSearchClear', panel ); - panel.searchFor = ''; - panel.filters = []; - panel.trigger( 'search:clear', panel ); - panel.renderHdas(); - } - $where.searchInput({ - initialVal : panel.searchFor, - name : 'history-search', - placeholder : 'search datasets', - classes : 'history-search', - onfirstsearch : onFirstSearch, - onsearch : onSearch, - onclear : onSearchClear - }); - return $where; - }, -//TODO: to hidden/shown plugin - showSearchControls : function( speed ){ - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var panel = this, - $searchControls = this.$el.find( '.history-search-controls' ), - $input = $searchControls.find( '.history-search-input' ); - // if it hasn't been rendered - do it now - if( !$input.children().size() ){ - this.setUpSearchInput( $input ); - //$searchControls.append( faIconButton({ - // title : _l( 'More search options' ), - // classes : 'history-search-advanced', - // faIcon : 'fa-ellipsis-horizontal' - //}) ); - } - // then slide open, focusing on the input, and persisting the setting when it's done - $searchControls.slideDown( speed, function(){ - $( this ).find( 'input' ).focus(); - panel.preferences.set( 'searching', true ); - }); - }, - hideSearchControls : function(){ - speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - var panel = this; - this.$el.find( '.history-search-controls' ).slideUp( speed, function(){ - panel.preferences.set( 'searching', false ); - }); - }, - - /** toggle showing/hiding the search controls (rendering first on the initial show) */ - toggleSearchControls : function( eventOrSpeed ){ - speed = ( jQuery.type( eventOrSpeed ) === 'number' )?( eventOrSpeed ):( this.fxSpeed ); - if( this.$el.find( '.history-search-controls' ).is( ':visible' ) ){ - this.hideSearchControls( speed ); - } else { - this.showSearchControls( speed ); - } - }, // ........................................................................ multi-select of hdas + /** show selectors on all visible hdas and associated controls */ showSelectors : function( speed ){ this.selecting = true; this.$el.find( '.history-dataset-actions' ).slideDown( speed ); @@ -1103,6 +342,7 @@ this.selectedHdaIds = []; }, + /** hide selectors on all visible hdas and associated controls */ hideSelectors : function( speed ){ this.selecting = false; this.$el.find( '.history-dataset-actions' ).slideUp( speed ); @@ -1112,6 +352,7 @@ this.selectedHdaIds = []; }, + /** show or hide selectors on all visible hdas and associated controls */ toggleSelectors : function( speed ){ if( !this.selecting ){ this.showSelectors( speed ); @@ -1120,245 +361,36 @@ } }, + /** select all visible hdas */ selectAllDatasets : function( event ){ _.each( this.hdaViews, function( view ){ view.select( event ); }); }, + /** deselect all visible hdas */ deselectAllDatasets : function( event ){ _.each( this.hdaViews, function( view ){ view.deselect( event ); }); }, + /** return an array of all currently selected hdas */ getSelectedHdaViews : function(){ return _.filter( this.hdaViews, function( v ){ return v.selected; }); }, + /** return an HdaCollection of the models of all currenly selected hdas */ getSelectedHdaCollection : function(){ return new hdaModel.HDACollection( _.map( this.getSelectedHdaViews(), function( hdaView ){ return hdaView.model; }), { historyId: this.model.id }); }, - // ........................................................................ loading indicator - /** hide the panel and display a loading indicator (in the panel's parent) when history model's are switched */ - showLoadingIndicator : function( msg, speed, callback ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - if( !this.indicator ){ - this.indicator = new LoadingIndicator( this.$el, this.$el.parent() ); - } - if( !this.$el.is( ':visible' ) ){ - this.indicator.show( 0, callback ); - } else { - this.$el.fadeOut( speed ); - this.indicator.show( msg, speed, callback ); - } - }, - - /** hide the loading indicator */ - hideLoadingIndicator : function( speed, callback ){ - speed = ( speed !== undefined )?( speed ):( this.fxSpeed ); - if( this.indicator ){ - this.indicator.hide( speed, callback ); - } - }, - - // ........................................................................ (error) messages - /** Display a message in the top of the panel. - * @param {String} type type of message ('done', 'error', 'warning') - * @param {String} msg the message to display - */ - displayMessage : function( type, msg, details ){ - //precondition: msgContainer must have been rendered even if there's no model - var panel = this; - //console.debug( 'displayMessage', type, msg, details ); - - this.scrollToTop(); - var $msgContainer = this.$el.find( this.msgsSelector ), - $msg = $( '<div/>' ).addClass( type + 'message' ).html( msg ); - //console.debug( ' ', $msgContainer ); - - if( !_.isEmpty( details ) ){ - var $detailsLink = $( '<a href="javascript:void(0)">Details</a>' ) - .click( function(){ - Galaxy.modal.show( panel.messageToModalOptions( type, msg, details ) ); - return false; - }); - $msg.append( ' ', $detailsLink ); - } - return $msgContainer.html( $msg ); - }, - - /** convert msg and details into modal options usable by Galaxy.modal */ - messageToModalOptions : function( type, msg, details ){ - // only error is fleshed out here - var panel = this, - $modalBody = $( '<div/>' ), - options = { title: 'Details' }; - - //TODO: to some util library - function objToTable( obj ){ - obj = _.omit( obj, _.functions( obj ) ); - return [ - '<table>', - _.map( obj, function( val, key ){ - val = ( _.isObject( val ) )?( objToTable( val ) ):( val ); - return '<tr><td style="vertical-align: top; color: grey">' + key + '</td>' - + '<td style="padding-left: 8px">' + val + '</td></tr>'; - }).join( '' ), - '</table>' - ].join( '' ); - } - - if( _.isObject( details ) ){ - options.body = $modalBody.append( objToTable( details ) ); - - } else { - options.body = $modalBody.html( details ); - } - options.buttons = { - 'Ok': function(){ - Galaxy.modal.hide(); - panel.clearMessages(); - } - //TODO: if( type === 'error' ){ options.buttons[ 'Report this error' ] = function(){} } - }; - return options; - }, - - /** Remove all messages from the panel. - */ - clearMessages : function(){ - var $msgContainer = this.$el.find( this.msgsSelector ); - $msgContainer.empty(); - }, - - // ........................................................................ scrolling - /** get the current scroll position of the panel in its parent */ - scrollPosition : function(){ - return this.$el.parent().scrollTop(); - }, - - /** set the current scroll position of the panel in its parent */ - scrollTo : function( pos ){ - this.$el.parent().scrollTop( pos ); - }, - - /** Scrolls the panel to the top. - * @returns {HistoryPanel} the panel - */ - scrollToTop : function(){ - this.$el.parent().scrollTop( 0 ); - return this; - }, - - /** Scrolls the panel (the enclosing container - in gen., the page) so that some object - * is displayed in the vertical middle. - * NOTE: if no size is given the panel will scroll to objTop (putting it at the top). - * @param {Number} objTop the top offset of the object to view - * @param {Number} objSize the size of the object to view - * @returns {HistoryPanel} the panel - */ - scrollIntoView : function( where, size ){ - if( !size ){ - this.$el.parent().parent().scrollTop( where ); - return this; - } - // otherwise, place the object in the vertical middle - var viewport = window, - panelContainer = this.$el.parent().parent(), - containerHeight = $( viewport ).innerHeight(), - middleOffset = ( containerHeight / 2 ) - ( size / 2 ); - - $( panelContainer ).scrollTop( where - middleOffset ); - return this; - }, - - /** Scrolls the panel to show the HDA with the given id. - * @param {String} id the id of HDA to scroll into view - * @returns {HistoryPanel} the panel - */ - scrollToId : function( id ){ - // do nothing if id not found - if( ( !id ) || ( !this.hdaViews[ id ] ) ){ - return this; - } - var $viewEl = this.hdaViews[ id ].$el; - this.scrollIntoView( $viewEl.offset().top, $viewEl.outerHeight() ); - return this; - }, - - /** Scrolls the panel to show the HDA with the given hid. - * @param {Integer} hid the hid of HDA to scroll into view - * @returns {HistoryPanel} the panel - */ - scrollToHid : function( hid ){ - var hda = this.model.hdas.getByHid( hid ); - // do nothing if hid not found - if( !hda ){ return this; } - return this.scrollToId( hda.id ); - }, - - // ........................................................................ external objects/MVC - //TODO: remove quota meter from panel and remove this - /** add listeners to an external quota meter (mvc/user/user-quotameter.js) */ - connectToQuotaMeter : function( quotaMeter ){ - if( !quotaMeter ){ - return this; - } - // show/hide the 'over quota message' in the history when the meter tells it to - this.listenTo( quotaMeter, 'quota:over', this.showQuotaMessage ); - this.listenTo( quotaMeter, 'quota:under', this.hideQuotaMessage ); - - // having to add this to handle re-render of hview while overquota (the above do not fire) - this.on( 'rendered rendered:initial', function(){ - if( quotaMeter && quotaMeter.isOverQuota() ){ - this.showQuotaMessage(); - } - }); - return this; - }, - -//TODO: this seems more like a per user message than a history message; IOW, this doesn't belong here - /** Show the over quota message (which happens to be in the history panel). - */ - showQuotaMessage : function(){ - var msg = this.$el.find( '.quota-message' ); - //this.log( this + ' showing quota message:', msg, userData ); - if( msg.is( ':hidden' ) ){ msg.slideDown( this.fxSpeed ); } - }, - -//TODO: this seems more like a per user message than a history message - /** Hide the over quota message (which happens to be in the history panel). - */ - hideQuotaMessage : function(){ - var msg = this.$el.find( '.quota-message' ); - //this.log( this + ' hiding quota message:', msg, userData ); - if( !msg.is( ':hidden' ) ){ msg.slideUp( this.fxSpeed ); } - }, - -//TODO: move show_deleted/hidden into panel from opt menu and remove this - /** add listeners to an external options menu (templates/webapps/galaxy/root/index.mako) */ - connectToOptionsMenu : function( optionsMenu ){ - if( !optionsMenu ){ - return this; - } - // set a visible indication in the popupmenu for show_hidden/deleted based on the currHistoryPanel's settings - this.on( 'new-storage', function( storage, panel ){ - if( optionsMenu && storage ){ - optionsMenu.findItemByHtml( _l( 'Include Deleted Datasets' ) ).checked = storage.get( 'show_deleted' ); - optionsMenu.findItemByHtml( _l( 'Include Hidden Datasets' ) ).checked = storage.get( 'show_hidden' ); - } - }); - return this; - }, - - /** Return a string rep of the history - */ + // ........................................................................ misc + /** Return a string rep of the history */ toString : function(){ return 'HistoryPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; } @@ -1372,6 +404,6 @@ //============================================================================== return { - HistoryPanel : HistoryPanel + HistoryPanel : HistoryPanel }; }); This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/82d6ee82d5d4/ Changeset: 82d6ee82d5d4 User: carlfeberhard Date: 2014-02-18 21:12:31 Summary: merge Affected #: 1 file diff -r 33812bcdc52393bf179dd501b4334be4ec4e97a7 -r 82d6ee82d5d4714eefdbce041f6c983a806a58d7 templates/webapps/galaxy/mobile/history/detail.mako --- a/templates/webapps/galaxy/mobile/history/detail.mako +++ b/templates/webapps/galaxy/mobile/history/detail.mako @@ -12,7 +12,7 @@ if data.state in ['no state','',None]: data_state = "queued" else: - data_state = data.state + data_state = str( data.state ) %><li id="historyItemContainer-${data.id}"> 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.

1 0

commit/galaxy-central: dan: Fix for server error caused by unicode substitution in url_for.
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e9d3248c6fc3/ Changeset: e9d3248c6fc3 User: dan Date: 2014-02-18 21:09:46 Summary: Fix for server error caused by unicode substitution in url_for. Affected #: 1 file diff -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 -r e9d3248c6fc312f8c7671a8e1233265c4ff0a0b1 templates/webapps/galaxy/mobile/history/detail.mako --- a/templates/webapps/galaxy/mobile/history/detail.mako +++ b/templates/webapps/galaxy/mobile/history/detail.mako @@ -12,7 +12,7 @@ if data.state in ['no state','',None]: data_state = "queued" else: - data_state = data.state + data_state = str( data.state ) %><li id="historyItemContainer-${data.id}"> 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.

1 0

commit/galaxy-central: guerler: Upload: Hide former upload tool
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26e37f6af3a8/ Changeset: 26e37f6af3a8 User: guerler Date: 2014-02-18 20:57:08 Summary: Upload: Hide former upload tool Affected #: 3 files diff -r c755326c2018efa988daebe96c355a32b6482018 -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -183,7 +183,7 @@ buttons : { 'Choose local file' : function() {self.uploadbox.select()}, 'Choose FTP file' : function() {self._eventFtp()}, - 'Create new file' : function() {self._eventCreate()}, + 'Paste/Fetch data' : function() {self._eventCreate()}, 'Start' : function() {self._eventStart()}, 'Pause' : function() {self._eventStop()}, 'Reset' : function() {self._eventReset()}, @@ -577,11 +577,11 @@ { this.modal.enableButton('Choose local file'); this.modal.enableButton('Choose FTP file'); - this.modal.enableButton('Create new file'); + this.modal.enableButton('Paste/Fetch data'); } else { this.modal.disableButton('Choose local file'); this.modal.disableButton('Choose FTP file'); - this.modal.disableButton('Create new file'); + this.modal.disableButton('Paste/Fetch data'); } // ftp button diff -r c755326c2018efa988daebe96c355a32b6482018 -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Paste/Fetch data":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Paste/Fetch data")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Paste/Fetch data")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file diff -r c755326c2018efa988daebe96c355a32b6482018 -r 26e37f6af3a8a090d9d6e923fa3e90acb0e64572 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,6 +1,7 @@ <?xml version="1.0"?><tool name="Upload File" id="upload1" version="1.1.4" workflow_compatible="false"> + <hidden>True</hidden><description> from your computer </description> 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.

1 0

commit/galaxy-central: guerler: Upload: Load user details on show
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c755326c2018/ Changeset: c755326c2018 User: guerler Date: 2014-02-18 19:21:03 Summary: Upload: Load user details on show Affected #: 2 files diff -r 5ea343bbc97bc1ebb8fa1bcd3e0df2889ef232ca -r c755326c2018efa988daebe96c355a32b6482018 static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -214,13 +214,16 @@ title : 'FTP files', container : button }); - - // setup info - this._updateScreen(); } // show modal this.modal.show(); + + // refresh + this._updateUser(); + + // setup info + this._updateScreen(); }, // @@ -526,9 +529,6 @@ // set screen _updateScreen: function () { - // refresh - this._updateUser(); - /* update on screen info */ diff -r 5ea343bbc97bc1ebb8fa1bcd3e0df2889ef232ca -r c755326c2018efa988daebe96c355a32b6482018 static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i});this._updateScreen()}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){this._updateUser();if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}this.modal.show();this._updateUser();this._updateScreen()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ 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.

1 0

commit/galaxy-central: guerler: Upload: Make upload available to anonymous users
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5ea343bbc97b/ Changeset: 5ea343bbc97b User: guerler Date: 2014-02-18 19:13:04 Summary: Upload: Make upload available to anonymous users Affected #: 5 files diff -r 05c93f3b424c372c14468f9aa25a79db88bfca24 -r 5ea343bbc97bc1ebb8fa1bcd3e0df2889ef232ca lib/galaxy/visualization/genomes.py --- a/lib/galaxy/visualization/genomes.py +++ b/lib/galaxy/visualization/genomes.py @@ -218,9 +218,10 @@ # Add user's custom keys to dbkeys. user_keys_dict = {} user = trans.get_user() - if 'dbkeys' in user.preferences: - user_keys_dict = from_json_string( user.preferences[ 'dbkeys' ] ) - dbkeys.extend( [ (attributes[ 'name' ], key ) for key, attributes in user_keys_dict.items() ] ) + if user: + if 'dbkeys' in user.preferences: + user_keys_dict = from_json_string( user.preferences[ 'dbkeys' ] ) + dbkeys.extend( [ (attributes[ 'name' ], key ) for key, attributes in user_keys_dict.items() ] ) # Add app keys to dbkeys. diff -r 05c93f3b424c372c14468f9aa25a79db88bfca24 -r 5ea343bbc97bc1ebb8fa1bcd3e0df2889ef232ca lib/galaxy/webapps/galaxy/api/genomes.py --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -14,7 +14,7 @@ RESTful controller for interactions with genome data. """ - @web.expose_api + @web.expose_api_anonymous def index( self, trans, **kwd ): """ GET /api/genomes: returns a list of installed genomes diff -r 05c93f3b424c372c14468f9aa25a79db88bfca24 -r 5ea343bbc97bc1ebb8fa1bcd3e0df2889ef232ca lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -64,7 +64,7 @@ trans.response.status = 500 return { 'error': str( exc ) } - @web.expose_api + @web.expose_api_anonymous def create( self, trans, payload, **kwd ): """ POST /api/tools diff -r 05c93f3b424c372c14468f9aa25a79db88bfca24 -r 5ea343bbc97bc1ebb8fa1bcd3e0df2889ef232ca static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -90,11 +90,6 @@ return; } - // check if logged in - if (!Galaxy.currUser.get('id')) { - return; - } - // create model this.ui_button = new UploadButton.Model({ icon : 'fa-upload', @@ -213,19 +208,15 @@ complete : function() { self._eventComplete() } }); + // add ftp file viewer + var button = this.modal.getButton('Choose FTP file'); + this.ftp = new Popover.View({ + title : 'FTP files', + container : button + }); + // setup info this._updateScreen(); - - // add ftp file viewer - if (this.options.ftp_upload_dir && this.options.ftp_upload_site) { - var button = this.modal.getButton('Choose FTP file'); - this.ftp = new Popover.View({ - title : 'FTP files', - container : button - }); - } else { - this.modal.hideButton('Choose FTP file'); - } } // show modal @@ -429,7 +420,7 @@ // // events triggered by this view // - + _eventFtp: function() { // check if popover is visible if (!this.ftp.visible) { @@ -476,9 +467,6 @@ this.ui_button.set('percentage', 0); this.ui_button.set('status', 'success'); - // backup current history - this.current_history = Galaxy.currHistoryPanel.model.get('id'); - // update running this.counter.running = this.counter.announce; this._updateScreen(); @@ -526,8 +514,21 @@ } }, + // update uset + _updateUser: function() { + // backup current history + this.current_user = Galaxy.currUser.get('id'); + this.current_history = null; + if (this.current_user) { + this.current_history = Galaxy.currHistoryPanel.model.get('id'); + } + }, + // set screen _updateScreen: function () { + // refresh + this._updateUser(); + /* update on screen info */ @@ -583,6 +584,13 @@ this.modal.disableButton('Create new file'); } + // ftp button + if (this.current_user && this.options.ftp_upload_dir && this.options.ftp_upload_site) { + this.modal.showButton('Choose FTP file'); + } else { + this.modal.hideButton('Choose FTP file'); + } + // table visibility if (this.counter.announce + this.counter.success + this.counter.error > 0) $(this.el).find('#upload-table').show(); diff -r 05c93f3b424c372c14468f9aa25a79db88bfca24 -r 5ea343bbc97bc1ebb8fa1bcd3e0df2889ef232ca static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i});this._updateScreen()}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateUser:function(){this.current_user=Galaxy.currUser.get("id");this.current_history=null;if(this.current_user){this.current_history=Galaxy.currHistoryPanel.model.get("id")}},_updateScreen:function(){this._updateUser();if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.current_user&&this.options.ftp_upload_dir&&this.options.ftp_upload_site){this.modal.showButton("Choose FTP file")}else{this.modal.hideButton("Choose FTP file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ 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.

1 0

commit/galaxy-central: dan: Fix for deleting uploading HDAs.
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/05c93f3b424c/ Changeset: 05c93f3b424c User: dan Date: 2014-02-18 18:57:39 Summary: Fix for deleting uploading HDAs. Affected #: 1 file diff -r 5c3d7c2346617774a4248b9ef990a3208e00576b -r 05c93f3b424c372c14468f9aa25a79db88bfca24 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 @@ -274,7 +274,9 @@ return { 'error': 'Anonymous users cannot edit datasets outside their current history' } else: payload = self._validate_and_parse_update_payload( payload ) - hda = self.get_dataset( trans, id, check_ownership=True, check_accessible=True, check_state=True ) + # only check_state if not deleting, otherwise cannot delete uploading files + check_state = not payload.get( 'deleted', False ) + hda = self.get_dataset( trans, id, check_ownership=True, check_accessible=True, check_state=check_state ) # get_dataset can return a string during an error if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ): changed = self.set_hda_from_dict( trans, hda, payload ) 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.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/05b757b20e06/ Changeset: 05b757b20e06 User: jmchilton Date: 2014-02-18 18:33:25 Summary: Random PEP-8 fixes to some api controllers. Affected #: 3 files diff -r a04725d3afedb65329b13bf5ba813e6381ec082f -r 05b757b20e06ee2667a3e910cf24e64f14915953 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -10,6 +10,7 @@ import logging log = logging.getLogger( __name__ ) + class LibrariesController( BaseAPIController ): @web.expose_api @@ -130,7 +131,7 @@ new_library['synopsis'] = synopsis new_library['id'] = encoded_id return new_library - + def edit( self, trans, encoded_id, payload, **kwd ): """ * PUT /api/libraries/{encoded_id} diff -r a04725d3afedb65329b13bf5ba813e6381ec082f -r 05b757b20e06ee2667a3e910cf24e64f14915953 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -2,7 +2,7 @@ API operations on the contents of a library. """ import logging -from galaxy import web , exceptions +from galaxy import web, exceptions from galaxy.model import ExtendedMetadata, ExtendedMetadataIndex from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems from galaxy.web.base.controller import UsesHistoryDatasetAssociationMixin @@ -11,6 +11,7 @@ log = logging.getLogger( __name__ ) + class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesHistoryDatasetAssociationMixin ): @@ -36,6 +37,7 @@ """ rval = [] current_user_roles = trans.get_current_user_roles() + def traverse( folder ): admin = trans.user_is_admin() rval = [] @@ -50,7 +52,9 @@ for ld in folder.datasets: if not admin: can_access = trans.app.security_agent.can_access_dataset( - current_user_roles, ld.library_dataset_dataset_association.dataset ) + current_user_roles, + ld.library_dataset_dataset_association.dataset + ) if (admin or can_access) and not ld.deleted: #log.debug( "type(folder): %s" % type( folder ) ) #log.debug( "type(api_path): %s; folder.api_path: %s" % ( type(folder.api_path), folder.api_path ) ) @@ -73,20 +77,20 @@ return "Invalid library id ( %s ) specified." % str( library_id ) #log.debug( "Root folder type: %s" % type( library.root_folder ) ) encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) - rval.append( dict( id = encoded_id, - type = 'folder', - name = '/', - url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) + rval.append( dict( id=encoded_id, + type='folder', + name='/', + url=url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) #log.debug( "Root folder attributes: %s" % str(dir(library.root_folder)) ) library.root_folder.api_path = '' for content in traverse( library.root_folder ): encoded_id = trans.security.encode_id( content.id ) if content.api_type == 'folder': encoded_id = 'F' + encoded_id - rval.append( dict( id = encoded_id, - type = content.api_type, - name = content.api_path, - url = url_for( 'library_content', library_id=library_id, id=encoded_id, ) ) ) + rval.append( dict( id=encoded_id, + type=content.api_type, + name=content.api_path, + url=url_for( 'library_content', library_id=library_id, id=encoded_id, ) ) ) return rval @web.expose_api diff -r a04725d3afedb65329b13bf5ba813e6381ec082f -r 05b757b20e06ee2667a3e910cf24e64f14915953 lib/galaxy/webapps/galaxy/api/roles.py --- a/lib/galaxy/webapps/galaxy/api/roles.py +++ b/lib/galaxy/webapps/galaxy/api/roles.py @@ -4,11 +4,12 @@ import logging from galaxy.web.base.controller import BaseAPIController, url_for from galaxy import web -from elementtree.ElementTree import XML log = logging.getLogger( __name__ ) + class RoleAPIController( BaseAPIController ): + @web.expose_api def index( self, trans, **kwd ): """ @@ -61,11 +62,11 @@ if not name or not description: trans.response.status = 400 return "Enter a valid name and a description" - if trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==name ).first(): + if trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name == name ).first(): trans.response.status = 400 return "A role with that name already exists" - role_type = trans.app.model.Role.types.ADMIN #TODO: allow non-admins to create roles + role_type = trans.app.model.Role.types.ADMIN # TODO: allow non-admins to create roles role = trans.app.model.Role( name=name, description=description, type=role_type ) trans.sa_session.add( role ) @@ -73,12 +74,15 @@ users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ] group_ids = payload.get( 'group_ids', [] ) groups = [ trans.sa_session.query( trans.model.Group ).get( trans.security.decode_id( i ) ) for i in group_ids ] + # Create the UserRoleAssociations for user in users: trans.app.security_agent.associate_user_role( user, role ) + # Create the GroupRoleAssociations for group in groups: trans.app.security_agent.associate_group_role( group, role ) + trans.sa_session.flush() encoded_id = trans.security.encode_id( role.id ) item = role.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id } ) https://bitbucket.org/galaxy/galaxy-central/commits/98253ff31a33/ Changeset: 98253ff31a33 User: jmchilton Date: 2014-02-18 18:33:28 Summary: Add note to job_conf.xml.sample_advanced about LWR+MQ. Affected #: 1 file diff -r 05b757b20e06ee2667a3e910cf24e64f14915953 -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -23,6 +23,11 @@  +  +  + </plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> https://bitbucket.org/galaxy/galaxy-central/commits/5c3d7c234661/ Changeset: 5c3d7c234661 User: jmchilton Date: 2014-02-18 18:33:28 Summary: Improvement to message queue driven LWR. At high-level there are two core enhancements here - ability to kill message queue driven LWR jobs (though due to regressions in latest galaxy release there is not longer a way to initiate this from the GUI I don't think) and additional state transition (LWR+MQ jobs will now transition from queue to running properly, previously they just went from queue to complete). A lot of other small changes to LWR client aimed at getting file size of lwr_client/client.py and lwr_client/manager.py under control - see LWR commit log for more details. This updates the LWR client through LWR changeset 2d9f333. Affected #: 9 files diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -52,7 +52,7 @@ try: client = self.get_client_from_state(job_state) - if not hasattr(client, 'get_status'): + if hasattr(self.client_manager, 'ensure_has_status_update_callback'): # Message queue implementation. # TODO: Very hacky now, refactor after Dannon merges in his @@ -60,7 +60,7 @@ # check_watched_item like this and instead a callback needs to # be issued post job recovery allowing a message queue # consumer to be setup. - self.client_manager.ensure_has_job_completes_callback(self.__async_complete) + self.client_manager.ensure_has_status_update_callback(self.__async_update) return job_state status = client.get_status() @@ -69,16 +69,20 @@ # either way we are done I guess. self.mark_as_finished(job_state) return None - if status == "complete": + job_state = self.__update_job_state_for_lwr_status(job_state, status) + return job_state + + def __update_job_state_for_lwr_status(self, job_state, lwr_status): + if lwr_status == "complete": self.mark_as_finished(job_state) return None - if status == "running" and not job_state.running: + if lwr_status == "running" and not job_state.running: job_state.running = True job_state.job_wrapper.change_state( model.Job.states.RUNNING ) return job_state - def __async_complete( self, final_status ): - job_id = final_status[ "job_id" ] + def __async_update( self, full_status ): + job_id = full_status[ "job_id" ] job_state = self.__find_watched_job( job_id ) if not job_state: # Probably finished too quickly, sleep and try again. @@ -88,9 +92,9 @@ sleep( 2 ) job_state = self.__find_watched_job( job_id ) if not job_state: - log.warn( "Failed to find job corresponding to final status %s in %s" % ( final_status, self.watched ) ) + log.warn( "Failed to find job corresponding to final status %s in %s" % ( full_status, self.watched ) ) else: - self.mark_as_finished( job_state ) + self.__update_job_state_for_lwr_status(job_state, full_status["status"]) def __find_watched_job( self, job_id ): found_job = None @@ -227,7 +231,7 @@ job_wrapper = job_state.job_wrapper try: client = self.get_client_from_state(job_state) - run_results = client.final_status() + run_results = client.full_status() stdout = run_results.get('stdout', '') stderr = run_results.get('stderr', '') @@ -251,7 +255,7 @@ except Exception: message = "Failed to communicate with remote job server." job_wrapper.fail( message, exception=True ) - log.exception("failure running job %d" % job_wrapper.job_id) + log.exception("failure finishing job %d" % job_wrapper.job_id) return if not LwrJobRunner.__remote_metadata( client ): self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -40,10 +40,15 @@ self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) self.__timeout = timeout + @property + def url(self): + return self.__url + def consume(self, queue_name, callback, check=True, connection_kwargs={}): queue = self.__queue(queue_name) with self.connection(self.__url, **connection_kwargs) as connection: with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): + log.debug("Consuming queue %s" % queue) while check: try: connection.drain_events(timeout=self.__timeout) @@ -54,6 +59,7 @@ with self.connection(self.__url) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) + log.debug("Publishing with key %s and payload %s" % (key, payload)) producer.publish( payload, serializer='json', diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -1,49 +1,18 @@ import os -import shutil -import json from json import dumps -from time import sleep from .destination import submit_params from .setup_handler import build as build_setup_handler from .job_directory import RemoteJobDirectory +from .decorators import parseJson +from .decorators import retry +from .util import copy +from .util import ensure_directory import logging log = logging.getLogger(__name__) CACHE_WAIT_SECONDS = 3 -MAX_RETRY_COUNT = 5 -RETRY_SLEEP_TIME = 0.1 - - -class parseJson(object): - - def __call__(self, func): - def replacement(*args, **kwargs): - response = func(*args, **kwargs) - return json.loads(response) - return replacement - - -class retry(object): - - def __call__(self, func): - - def replacement(*args, **kwargs): - max_count = MAX_RETRY_COUNT - count = 0 - while True: - count += 1 - try: - return func(*args, **kwargs) - except: - if count >= max_count: - raise - else: - sleep(RETRY_SLEEP_TIME) - continue - - return replacement class OutputNotFoundException(Exception): @@ -111,17 +80,78 @@ super(JobClient, self).__init__(destination_params, job_id) self.job_manager_interface = job_manager_interface - def _raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): - return self.job_manager_interface.execute(command, args, data, input_path, output_path) + def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): + """ + Queue up the execution of the supplied `command_line` on the remote + server. Called launch for historical reasons, should be renamed to + enqueue or something like that. - @property - def _submit_params(self): - return submit_params(self.destination_params) + **Parameters** + + command_line : str + Command to execute. + """ + launch_params = dict(command_line=command_line, job_id=self.job_id) + submit_params_dict = submit_params(self.destination_params) + if submit_params_dict: + launch_params['params'] = dumps(submit_params_dict) + if requirements: + launch_params['requirements'] = dumps([requirement.to_dict() for requirement in requirements]) + if remote_staging: + launch_params['remote_staging'] = dumps(remote_staging) + if job_config and self.setup_handler.local: + # Setup not yet called, job properties were inferred from + # destination arguments. Hence, must have LWR setup job + # before queueing. + setup_params = _setup_params_from_job_config(job_config) + launch_params["setup_params"] = dumps(setup_params) + return self._raw_execute("launch", launch_params) + + def full_status(self): + """ Return a dictionary summarizing final state of job. + """ + return self.raw_check_complete() + + def kill(self): + """ + Cancel remote job, either removing from the queue or killing it. + """ + return self._raw_execute("kill", {"job_id": self.job_id}) + + @retry() + @parseJson() + def raw_check_complete(self): + """ + Get check_complete response from the remote server. + """ + check_complete_response = self._raw_execute("check_complete", {"job_id": self.job_id}) + return check_complete_response + + def get_status(self): + check_complete_response = self.raw_check_complete() + # Older LWR instances won't set status so use 'complete', at some + # point drop backward compatibility. + status = check_complete_response.get("status", None) + if status in ["status", None]: + # LEGACY: Bug in certains older LWR instances returned literal + # "status". + complete = check_complete_response["complete"] == "true" + old_status = "complete" if complete else "running" + status = old_status + return status + + def clean(self): + """ + Cleanup the remote job. + """ + self._raw_execute("clean", {"job_id": self.job_id}) @parseJson() - def input_path(self, path, input_type, name=None): - args = {"job_id": self.job_id, "name": name, "input_type": input_type} - return self._raw_execute('input_path', args) + def remote_setup(self, **setup_args): + """ + Setup remote LWR server to run this job. + """ + return self._raw_execute("setup", setup_args) def put_file(self, path, input_type, name=None, contents=None, action_type='transfer'): if not name: @@ -134,9 +164,80 @@ return self._upload_file(args, contents, input_path) elif action_type == 'copy': lwr_path = self._raw_execute('input_path', args) - self._copy(path, lwr_path) + copy(path, lwr_path) return {'path': lwr_path} + def fetch_output(self, path, name, working_directory, action_type, output_type): + """ + Fetch (transfer, copy, etc...) an output from the remote LWR server. + + **Parameters** + + path : str + Local path of the dataset. + name : str + Remote name of file (i.e. path relative to remote staging output + or working directory). + working_directory : str + Local working_directory for the job. + action_type : str + Where to find file on LWR (output_workdir or output). legacy is also + an option in this case LWR is asked for location - this will only be + used if targetting an older LWR server that didn't return statuses + allowing this to be inferred. + """ + if output_type == 'legacy': + self._fetch_output_legacy(path, working_directory, action_type=action_type) + elif output_type == 'output_workdir': + self._fetch_work_dir_output(name, working_directory, path, action_type=action_type) + elif output_type == 'output': + self._fetch_output(path=path, name=name, action_type=action_type) + else: + raise Exception("Unknown output_type %s" % output_type) + + def _raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): + return self.job_manager_interface.execute(command, args, data, input_path, output_path) + + # Deprecated + def _fetch_output_legacy(self, path, working_directory, action_type='transfer'): + # Needs to determine if output is task/working directory or standard. + name = os.path.basename(path) + + output_type = self._get_output_type(name) + if output_type == "none": + # Just make sure the file was created. + if not os.path.exists(path): + raise OutputNotFoundException(path) + return + elif output_type in ["task"]: + path = os.path.join(working_directory, name) + + self.__populate_output_path(name, path, output_type, action_type) + + def _fetch_output(self, path, name=None, check_exists_remotely=False, action_type='transfer'): + if not name: + # Extra files will send in the path. + name = os.path.basename(path) + + output_type = "direct" # Task/from_work_dir outputs now handled with fetch_work_dir_output + self.__populate_output_path(name, path, output_type, action_type) + + def _fetch_work_dir_output(self, name, working_directory, output_path, action_type='transfer'): + ensure_directory(output_path) + if action_type == 'transfer': + self.__raw_download_output(name, self.job_id, "work_dir", output_path) + else: # Even if action is none - LWR has a different work_dir so this needs to be copied. + lwr_path = self._output_path(name, self.job_id, 'work_dir')['path'] + copy(lwr_path, output_path) + + def __populate_output_path(self, name, output_path, output_type, action_type): + ensure_directory(output_path) + if action_type == 'transfer': + self.__raw_download_output(name, self.job_id, output_type, output_path) + elif action_type == 'copy': + lwr_path = self._output_path(name, self.job_id, output_type)['path'] + copy(lwr_path, output_path) + @parseJson() def _upload_file(self, args, contents, input_path): return self._raw_execute(self._upload_file_action(args), args, contents, input_path) @@ -163,75 +264,6 @@ return self._raw_execute("get_output_type", {"name": name, "job_id": self.job_id}) - # Deprecated - def fetch_output_legacy(self, path, working_directory, action_type='transfer'): - # Needs to determine if output is task/working directory or standard. - name = os.path.basename(path) - - output_type = self._get_output_type(name) - if output_type == "none": - # Just make sure the file was created. - if not os.path.exists(path): - raise OutputNotFoundException(path) - return - elif output_type in ["task"]: - path = os.path.join(working_directory, name) - - self.__populate_output_path(name, path, output_type, action_type) - - def fetch_output(self, path, name=None, check_exists_remotely=False, action_type='transfer'): - """ - Download an output dataset from the remote server. - - **Parameters** - - path : str - Local path of the dataset. - working_directory : str - Local working_directory for the job. - """ - - if not name: - # Extra files will send in the path. - name = os.path.basename(path) - - output_type = "direct" # Task/from_work_dir outputs now handled with fetch_work_dir_output - self.__populate_output_path(name, path, output_type, action_type) - - def __populate_output_path(self, name, output_path, output_type, action_type): - self.__ensure_directory(output_path) - if action_type == 'transfer': - self.__raw_download_output(name, self.job_id, output_type, output_path) - elif action_type == 'copy': - lwr_path = self._output_path(name, self.job_id, output_type)['path'] - self._copy(lwr_path, output_path) - - def fetch_work_dir_output(self, name, working_directory, output_path, action_type='transfer'): - """ - Download an output dataset specified with from_work_dir from the - remote server. - - **Parameters** - - name : str - Path in job's working_directory to find output in. - working_directory : str - Local working_directory for the job. - output_path : str - Full path to output dataset. - """ - self.__ensure_directory(output_path) - if action_type == 'transfer': - self.__raw_download_output(name, self.job_id, "work_dir", output_path) - else: # Even if action is none - LWR has a different work_dir so this needs to be copied. - lwr_path = self._output_path(name, self.job_id, 'work_dir')['path'] - self._copy(lwr_path, output_path) - - def __ensure_directory(self, output_path): - output_path_directory = os.path.dirname(output_path) - if not os.path.exists(output_path_directory): - os.makedirs(output_path_directory) - @parseJson() def _output_path(self, name, job_id, output_type): return self._raw_execute("output_path", @@ -248,107 +280,6 @@ } self._raw_execute("download_output", output_params, output_path=output_path) - def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): - """ - Queue up the execution of the supplied `command_line` on the remote - server. Called launch for historical reasons, should be renamed to - enqueue or something like that. - - **Parameters** - - command_line : str - Command to execute. - """ - launch_params = dict(command_line=command_line, job_id=self.job_id) - submit_params = self._submit_params - if submit_params: - launch_params['params'] = dumps(submit_params) - if requirements: - launch_params['requirements'] = dumps([requirement.to_dict() for requirement in requirements]) - if remote_staging: - launch_params['remote_staging'] = dumps(remote_staging) - if job_config and self.setup_handler.local: - # Setup not yet called, job properties were inferred from - # destination arguments. Hence, must have LWR setup job - # before queueing. - setup_params = _setup_params_from_job_config(job_config) - launch_params["setup_params"] = dumps(setup_params) - return self._raw_execute("launch", launch_params) - - def final_status(self): - """ Return a dictionary summarizing final state of job. - """ - return self.raw_check_complete() - - def kill(self): - """ - Cancel remote job, either removing from the queue or killing it. - """ - return self._raw_execute("kill", {"job_id": self.job_id}) - - def wait(self, max_seconds=None): - """ - Wait for job to finish. - """ - i = 0 - while max_seconds is None or i < max_seconds: - complete_response = self.raw_check_complete() - if complete_response["complete"] == "true": - print complete_response - return complete_response - else: - print complete_response - sleep(1) - i += 1 - - @parseJson() - def raw_check_complete(self): - """ - Get check_complete response from the remote server. - """ - check_complete_response = self._raw_execute("check_complete", {"job_id": self.job_id}) - return check_complete_response - - def check_complete(self, response=None): - """ - Return boolean indicating whether the job is complete. - """ - if response is None: - response = self.raw_check_complete() - return response["complete"] == "true" - - @retry() - def get_status(self): - check_complete_response = self.raw_check_complete() - # Older LWR instances won't set status so use 'complete', at some - # point drop backward compatibility. - status = check_complete_response.get("status", None) - # Bug in certains older LWR instances returned literal "status". - if status in ["status", None]: - complete = self.check_complete(check_complete_response) - old_status = "complete" if complete else "running" - status = old_status - return status - - def clean(self): - """ - Cleanup the remote job. - """ - self._raw_execute("clean", {"job_id": self.job_id}) - - @parseJson() - def remote_setup(self, **setup_args): - """ - Setup remote LWR server to run this job. - """ - return self._raw_execute("setup", setup_args) - - def _copy(self, source, destination): - source = os.path.abspath(source) - destination = os.path.abspath(destination) - if source != destination: - shutil.copyfile(source, destination) - class MessageJobClient(BaseJobClient): @@ -379,16 +310,16 @@ return self.client_manager.exchange.publish("setup", launch_params) def clean(self): - del self.client_manager.final_status_cache[self.job_id] + del self.client_manager.status_cache[self.job_id] - def final_status(self): - final_status = self.client_manager.final_status_cache.get(self.job_id, None) - if final_status is None: - raise Exception("final_status() called before a final status was properly cached with cilent manager.") - return final_status + def full_status(self): + full_status = self.client_manager.status_cache.get(self.job_id, None) + if full_status is None: + raise Exception("full_status() called before a final status was properly cached with cilent manager.") + return full_status def kill(self): - log.warn("Kill not yet implemented with message queue driven LWR jobs.") + self.client_manager.exchange.publish("kill", dict(job_id=self.job_id)) class InputCachingJobClient(JobClient): @@ -443,55 +374,3 @@ tool_id=tool_id, tool_version=tool_version ) - - -class ObjectStoreClient(object): - - def __init__(self, lwr_interface): - self.lwr_interface = lwr_interface - - @parseJson() - def exists(self, **kwds): - return self._raw_execute("object_store_exists", args=self.__data(**kwds)) - - @parseJson() - def file_ready(self, **kwds): - return self._raw_execute("object_store_file_ready", args=self.__data(**kwds)) - - @parseJson() - def create(self, **kwds): - return self._raw_execute("object_store_create", args=self.__data(**kwds)) - - @parseJson() - def empty(self, **kwds): - return self._raw_execute("object_store_empty", args=self.__data(**kwds)) - - @parseJson() - def size(self, **kwds): - return self._raw_execute("object_store_size", args=self.__data(**kwds)) - - @parseJson() - def delete(self, **kwds): - return self._raw_execute("object_store_delete", args=self.__data(**kwds)) - - @parseJson() - def get_data(self, **kwds): - return self._raw_execute("object_store_get_data", args=self.__data(**kwds)) - - @parseJson() - def get_filename(self, **kwds): - return self._raw_execute("object_store_get_filename", args=self.__data(**kwds)) - - @parseJson() - def update_from_file(self, **kwds): - return self._raw_execute("object_store_update_from_file", args=self.__data(**kwds)) - - @parseJson() - def get_store_usage_percent(self): - return self._raw_execute("object_store_get_store_usage_percent", args={}) - - def __data(self, **kwds): - return kwds - - def _raw_execute(self, command, args={}): - return self.lwr_interface.execute(command, args, data=None, input_path=None, output_path=None) diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr_client/decorators.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/decorators.py @@ -0,0 +1,35 @@ +import time +import json + +MAX_RETRY_COUNT = 5 +RETRY_SLEEP_TIME = 0.1 + + +class parseJson(object): + + def __call__(self, func): + def replacement(*args, **kwargs): + response = func(*args, **kwargs) + return json.loads(response) + return replacement + + +class retry(object): + + def __call__(self, func): + + def replacement(*args, **kwargs): + max_count = MAX_RETRY_COUNT + count = 0 + while True: + count += 1 + try: + return func(*args, **kwargs) + except: + if count >= max_count: + raise + else: + time.sleep(RETRY_SLEEP_TIME) + continue + + return replacement diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr_client/interface.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/interface.py @@ -0,0 +1,97 @@ +from abc import ABCMeta +from abc import abstractmethod +try: + from StringIO import StringIO as BytesIO +except ImportError: + from io import BytesIO +try: + from six import text_type +except ImportError: + from galaxy.util import unicodify as text_type +try: + from urllib import urlencode +except ImportError: + from urllib.parse import urlencode + + +class LwrInteface(object): + """ + Abstract base class describes how synchronous client communicates with + (potentially remote) LWR procedures. Obvious implementation is HTTP based + but LWR objects wrapped in routes can also be directly communicated with + if in memory. + """ + __metaclass__ = ABCMeta + + @abstractmethod + def execute(self, command, args={}, data=None, input_path=None, output_path=None): + """ + Execute the correspond command against configured LWR job manager. Arguments are + method parameters and data or input_path describe essentially POST bodies. If command + results in a file, resulting path should be specified as output_path. + """ + + +class HttpLwrInterface(LwrInteface): + + def __init__(self, destination_params, transport): + self.transport = transport + self.remote_host = destination_params.get("url") + assert self.remote_host is not None, "Failed to determine url for LWR client." + self.private_key = destination_params.get("private_token", None) + + def execute(self, command, args={}, data=None, input_path=None, output_path=None): + url = self.__build_url(command, args) + response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) + return response + + def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key + arg_bytes = dict([(k, text_type(args[k]).encode('utf-8')) for k in args]) + data = urlencode(arg_bytes) + url = self.remote_host + command + "?" + data + return url + + +class LocalLwrInterface(LwrInteface): + + def __init__(self, destination_params, job_manager=None, file_cache=None, object_store=None): + self.job_manager = job_manager + self.file_cache = file_cache + self.object_store = object_store + + def __app_args(self): + ## Arguments that would be specified from LwrApp if running + ## in web server. + return { + 'manager': self.job_manager, + 'file_cache': self.file_cache, + 'object_store': self.object_store, + 'ip': None + } + + def execute(self, command, args={}, data=None, input_path=None, output_path=None): + # If data set, should be unicode (on Python 2) or str (on Python 3). + from lwr import routes + from lwr.framework import build_func_args + controller = getattr(routes, command) + action = controller.func + body_args = dict(body=self.__build_body(data, input_path)) + args = build_func_args(action, args.copy(), self.__app_args(), body_args) + result = action(**args) + if controller.response_type != 'file': + return controller.body(result) + else: + # TODO: Add to Galaxy. + from galaxy.util import copy_to_path + with open(result, 'rb') as result_file: + copy_to_path(result_file, output_path) + + def __build_body(self, data, input_path): + if data is not None: + return BytesIO(data.encode('utf-8')) + elif input_path is not None: + return open(input_path, 'rb') + else: + return None diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -1,27 +1,16 @@ -from abc import ABCMeta, abstractmethod import threading try: from Queue import Queue except ImportError: from queue import Queue from os import getenv -try: - from urllib import urlencode -except ImportError: - from urllib.parse import urlencode -try: - from StringIO import StringIO as BytesIO -except ImportError: - from io import BytesIO -try: - from six import text_type -except ImportError: - from galaxy.util import unicodify as text_type from .client import JobClient from .client import InputCachingJobClient -from .client import ObjectStoreClient from .client import MessageJobClient +from .interface import HttpLwrInterface +from .interface import LocalLwrInterface +from .object_client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager from .destination import url_to_destination_params @@ -87,12 +76,12 @@ self.url = kwds.get('url') self.manager_name = kwds.get("manager", "_default_") self.exchange = LwrExchange(self.url, self.manager_name) - self.final_status_cache = {} + self.status_cache = {} self.callback_lock = threading.Lock() self.callback_thread = None self.active = True - def ensure_has_job_completes_callback(self, callback): + def ensure_has_status_update_callback(self, callback): with self.callback_lock: if self.callback_thread is not None: return @@ -100,17 +89,17 @@ def callback_wrapper(body, message): try: if "job_id" in body: - self.final_status_cache[body["job_id"]] = body + self.status_cache[body["job_id"]] = body callback(body) except Exception: log.exception("Failure processing job status update message.") message.ack() def run(): - self.exchange.consume("complete", callback_wrapper, check=self) + self.exchange.consume("status_update", callback_wrapper, check=self) thread = threading.Thread( - name="lwr_client_%s_complete_callback" % self.manager_name, + name="lwr_client_%s_status_update_callback" % self.manager_name, target=run ) thread.daemon = False # Lets not interrupt processing of this. @@ -148,87 +137,6 @@ return ObjectStoreClient(interface) -class JobManagerInteface(object): - """ - Abstract base class describes how client communicates with remote job - manager. - """ - __metaclass__ = ABCMeta - - @abstractmethod - def execute(self, command, args={}, data=None, input_path=None, output_path=None): - """ - Execute the correspond command against configured LWR job manager. Arguments are - method parameters and data or input_path describe essentially POST bodies. If command - results in a file, resulting path should be specified as output_path. - """ - - -class HttpLwrInterface(object): - - def __init__(self, destination_params, transport): - self.transport = transport - self.remote_host = destination_params.get("url") - assert self.remote_host is not None, "Failed to determine url for LWR client." - self.private_key = destination_params.get("private_token", None) - - def execute(self, command, args={}, data=None, input_path=None, output_path=None): - url = self.__build_url(command, args) - response = self.transport.execute(url, data=data, input_path=input_path, output_path=output_path) - return response - - def __build_url(self, command, args): - if self.private_key: - args["private_key"] = self.private_key - arg_bytes = dict([(k, text_type(args[k]).encode('utf-8')) for k in args]) - data = urlencode(arg_bytes) - url = self.remote_host + command + "?" + data - return url - - -class LocalLwrInterface(object): - - def __init__(self, destination_params, job_manager=None, file_cache=None, object_store=None): - self.job_manager = job_manager - self.file_cache = file_cache - self.object_store = object_store - - def __app_args(self): - ## Arguments that would be specified from LwrApp if running - ## in web server. - return { - 'manager': self.job_manager, - 'file_cache': self.file_cache, - 'object_store': self.object_store, - 'ip': None - } - - def execute(self, command, args={}, data=None, input_path=None, output_path=None): - # If data set, should be unicode (on Python 2) or str (on Python 3). - from lwr import routes - from lwr.framework import build_func_args - controller = getattr(routes, command) - action = controller.func - body_args = dict(body=self.__build_body(data, input_path)) - args = build_func_args(action, args.copy(), self.__app_args(), body_args) - result = action(**args) - if controller.response_type != 'file': - return controller.body(result) - else: - # TODO: Add to Galaxy. - from galaxy.util import copy_to_path - with open(result, 'rb') as result_file: - copy_to_path(result_file, output_path) - - def __build_body(self, data, input_path): - if data is not None: - return BytesIO(data.encode('utf-8')) - elif input_path is not None: - return open(input_path, 'rb') - else: - return None - - class ClientCacher(object): def __init__(self, **kwds): diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr_client/object_client.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/object_client.py @@ -0,0 +1,53 @@ +from .decorators import parseJson + + +class ObjectStoreClient(object): + + def __init__(self, lwr_interface): + self.lwr_interface = lwr_interface + + @parseJson() + def exists(self, **kwds): + return self._raw_execute("object_store_exists", args=self.__data(**kwds)) + + @parseJson() + def file_ready(self, **kwds): + return self._raw_execute("object_store_file_ready", args=self.__data(**kwds)) + + @parseJson() + def create(self, **kwds): + return self._raw_execute("object_store_create", args=self.__data(**kwds)) + + @parseJson() + def empty(self, **kwds): + return self._raw_execute("object_store_empty", args=self.__data(**kwds)) + + @parseJson() + def size(self, **kwds): + return self._raw_execute("object_store_size", args=self.__data(**kwds)) + + @parseJson() + def delete(self, **kwds): + return self._raw_execute("object_store_delete", args=self.__data(**kwds)) + + @parseJson() + def get_data(self, **kwds): + return self._raw_execute("object_store_get_data", args=self.__data(**kwds)) + + @parseJson() + def get_filename(self, **kwds): + return self._raw_execute("object_store_get_filename", args=self.__data(**kwds)) + + @parseJson() + def update_from_file(self, **kwds): + return self._raw_execute("object_store_update_from_file", args=self.__data(**kwds)) + + @parseJson() + def get_store_usage_percent(self): + return self._raw_execute("object_store_get_store_usage_percent", args={}) + + def __data(self, **kwds): + return kwds + + def _raw_execute(self, command, args={}): + return self.lwr_interface.execute(command, args, data=None, input_path=None, output_path=None) diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr_client/staging/down.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/down.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/down.py @@ -41,15 +41,14 @@ if not action.staging_action_local: return False - path = action.path - if output_type == 'legacy': - working_directory = results_collector.client_outputs.working_directory - self.client.fetch_output_legacy(path, working_directory, action_type=action.action_type) - elif output_type == 'output_workdir': - working_directory = results_collector.client_outputs.working_directory - self.client.fetch_work_dir_output(name, working_directory, path, action_type=action.action_type) - elif output_type == 'output': - self.client.fetch_output(path=path, name=name, action_type=action.action_type) + working_directory = results_collector.client_outputs.working_directory + self.client.fetch_output( + path=action.path, + name=name, + working_directory=working_directory, + output_type=output_type, + action_type=action.action_type + ) return True diff -r 98253ff31a334d01eb2ee28e10c637f71c1ba6f3 -r 5c3d7c2346617774a4248b9ef990a3208e00576b lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -6,6 +6,7 @@ from os.path import join import os.path import hashlib +import shutil def unique_path_prefix(path): @@ -14,6 +15,22 @@ return m.hexdigest() +def copy(source, destination): + """ Copy file from source to destination if needed (skip if source + is destination). + """ + source = os.path.abspath(source) + destination = os.path.abspath(destination) + if source != destination: + shutil.copyfile(source, destination) + + +def ensure_directory(file_path): + directory = os.path.dirname(file_path) + if not os.path.exists(directory): + os.makedirs(directory) + + def directory_files(directory): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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1 0

commit/galaxy-central: carlfeberhard: Tagging: prevent intialization error on tag autocomplete (http://stackoverflow.com/questions/21549126/error-cannot-call-methods-on-autocomplete-prior-to-initialization-attempted-to)
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a04725d3afed/ Changeset: a04725d3afed User: carlfeberhard Date: 2014-02-18 17:55:34 Summary: Tagging: prevent intialization error on tag autocomplete (http://stackoverflow.com/questions/21549126/error-cannot-call-methods-on-au…) Affected #: 1 file diff -r a9fb2779dd6948fb94d820dce89ccc70335e6c47 -r a04725d3afedb65329b13bf5ba813e6381ec082f templates/tagging_common.mako --- a/templates/tagging_common.mako +++ b/templates/tagging_common.mako @@ -211,7 +211,7 @@ use_toggle_link: ${iff( use_toggle_link, 'true', 'false' )} }; - $('#${elt_id}').autocomplete_tagging(options); + $('#${elt_id}').find( 'input' ).autocomplete_tagging(options); </script> ## Use style to hide/display the tag area. 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: Add kombu, amqp, anyjson eggs.
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a9fb2779dd69/ Changeset: a9fb2779dd69 User: dannon Date: 2014-02-18 17:47:23 Summary: Add kombu, amqp, anyjson eggs. Affected #: 1 file diff -r 3a5251e288011f02eff318a4dd88d76af4edcfd3 -r a9fb2779dd6948fb94d820dce89ccc70335e6c47 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -32,7 +32,9 @@ ; msgpack_python = 0.2.4 [eggs:noplatform] +amqp = 1.4.3 amqplib = 0.6.1 +anyjson = 0.3.3 Beaker = 1.4 boto = 2.5.2 decorator = 3.1.2 @@ -41,6 +43,7 @@ elementtree = 1.2.6_20050316 Fabric = 1.7.0 GeneTrack = 2.0.0_beta_1 +kombu = 3.0.12 lrucache = 0.2 Mako = 0.4.1 nose = 0.11.1 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: HDA model: allow copying the purged attribute; History model: allow copying all datasets (including purged); History imp: change query param flag 'include_deleted' to 'all_datasets', send to History model copy; history/view: incorporate 'all_datasets' flag in import button
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3a5251e28801/ Changeset: 3a5251e28801 User: carlfeberhard Date: 2014-02-18 16:44:43 Summary: HDA model: allow copying the purged attribute; History model: allow copying all datasets (including purged); History imp: change query param flag 'include_deleted' to 'all_datasets', send to History model copy; history/view: incorporate 'all_datasets' flag in import button Affected #: 3 files diff -r 48f57ba4faed584929ab3ef31aa59f663d84a411 -r 3a5251e288011f02eff318a4dd88d76af4edcfd3 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -822,7 +822,12 @@ self.datasets.append( dataset ) return dataset - def copy( self, name=None, target_user=None, activatable=False ): + def copy( self, name=None, target_user=None, activatable=False, all_datasets=False ): + """ + Return a copy of this history using the given `name` and `target_user`. + If `activatable`, copy only non-deleted datasets. If `all_datasets`, copy + non-deleted, deleted, and purged datasets. + """ # Create new history. if not name: name = self.name @@ -845,6 +850,8 @@ # Copy HDAs. if activatable: hdas = self.activatable_datasets + elif all_datasets: + hdas = self.datasets else: hdas = self.active_datasets for hda in hdas: @@ -1682,6 +1689,9 @@ deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association=self ) + # update init non-keywords as well + hda.purged = self.purged + object_session( self ).add( hda ) object_session( self ).flush() hda.set_size() diff -r 48f57ba4faed584929ab3ef31aa59f663d84a411 -r 3a5251e288011f02eff318a4dd88d76af4edcfd3 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -783,8 +783,8 @@ else: referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) - # include activatable/deleted datasets when copying? - include_deleted = util.string_as_bool( kwd.get( 'include_deleted', False ) ) + # include all datasets when copying? + all_datasets = util.string_as_bool( kwd.get( 'all_datasets', False ) ) # Do import. if not id: @@ -799,7 +799,7 @@ #dan: I can import my own history. #if import_history.user_id == user.id: # return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) - new_history = import_history.copy( target_user=user, activatable=include_deleted ) + new_history = import_history.copy( target_user=user, all_datasets=all_datasets ) new_history.name = "imported: " + new_history.name new_history.user_id = user.id galaxy_session = trans.get_galaxy_session() diff -r 48f57ba4faed584929ab3ef31aa59f663d84a411 -r 3a5251e288011f02eff318a4dd88d76af4edcfd3 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -98,7 +98,7 @@ %> %if not history[ 'purged' ]: <a id="import" class="btn btn-default" style="display: none;" - href="${h.url_for( controller='history', action='imp', id=history['id'], include_deleted=show_deleted )}"> + href="${h.url_for( controller='history', action='imp', id=history['id'], all_datasets=show_deleted )}"> ${_('Import and start using history')} </a> %endif @@ -133,7 +133,7 @@ // a bit hacky var href = $importBtn.attr( 'href' ), includeDeleted = $( this ).modeButton()[0].getMode().mode === 'exclude'; - href = href.replace( /include_deleted=True|False/, ( includeDeleted )?( 'True' ):( 'False' ) ); + href = href.replace( /all_datasets=True|False/, ( includeDeleted )?( 'True' ):( 'False' ) ); $importBtn.attr( 'href', href ); $importBtn.text( includeDeleted ? _l( 'Import with deleted datasets and start using history' ) : _l( 'Import and start using history' ) ); 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: jmchilton: Fix for recent LWR message queue commit.
by commits-noreply＠bitbucket.org 18 Feb '14

18 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/48f57ba4faed/ Changeset: 48f57ba4faed User: jmchilton Date: 2014-02-18 13:32:08 Summary: Fix for recent LWR message queue commit. Was always trying to bind to message queue. Affected #: 1 file diff -r 75b13d642f94b9ff6ec7c3c3713ad1177b243bd3 -r 48f57ba4faed584929ab3ef31aa59f663d84a411 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -37,7 +37,7 @@ def build_client_manager(**kwargs): if 'job_manager' in kwargs: return ClientManager(**kwargs) # TODO: Consider more separation here. - elif 'url' in kwargs: + elif kwargs.get('url', None): return MessageQueueClientManager(**kwargs) else: return ClientManager(**kwargs) 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: jmchilton: Allow LWR runner to publish/consume messages via message queue.
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/75b13d642f94/ Changeset: 75b13d642f94 User: jmchilton Date: 2014-02-18 04:26:49 Summary: Allow LWR runner to publish/consume messages via message queue. To use LWR via message queue, ensure each such destination defines "default_file_action" as "remote_copy" and the LWR base staging directory pointed to by the "jobs_directory" parameter. Finally add a "url" argument to LWR job runner plugin in job_conf.xml specifing the amqp URL to target (by default this will target the default ("_default_") LWR job manager - this can be overridden by specifing a "manager" attribute the plugin element in job_conf.xml). Some of the implementation details here are bit hacky now to localize changes to LWR, once Dannon has merged his work - a new job runner base class or option should be implemented to account for this truely asynchronous job running implementation. (Comments inline about this.) This updates the LWR client through LWR changeset 59ad1ea03448. Affected #: 3 files diff -r 7d649885e3259f3359e8c3816315c60e958c1518 -r 75b13d642f94b9ff6ec7c3c3713ad1177b243bd3 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -35,12 +35,13 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers, transport=None, cache=None ): + def __init__( self, app, nworkers, transport=None, cache=None, url=None ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) + self.async_status_updates = dict() self._init_monitor_thread() self._init_worker_threads() - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache)} + client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url} self.client_manager = build_client_manager(**client_manager_kwargs) def url_to_destination( self, url ): @@ -50,6 +51,18 @@ def check_watched_item(self, job_state): try: client = self.get_client_from_state(job_state) + + if not hasattr(client, 'get_status'): + # Message queue implementation. + + # TODO: Very hacky now, refactor after Dannon merges in his + # message queue work, runners need the ability to disable + # check_watched_item like this and instead a callback needs to + # be issued post job recovery allowing a message queue + # consumer to be setup. + self.client_manager.ensure_has_job_completes_callback(self.__async_complete) + return job_state + status = client.get_status() except Exception: # An orphaned job was put into the queue at app startup, so remote server went down @@ -64,6 +77,29 @@ job_state.job_wrapper.change_state( model.Job.states.RUNNING ) return job_state + def __async_complete( self, final_status ): + job_id = final_status[ "job_id" ] + job_state = self.__find_watched_job( job_id ) + if not job_state: + # Probably finished too quickly, sleep and try again. + # Kind of a hack, why does monitor queue need to no wait + # get and sleep instead of doing a busy wait that would + # respond immediately. + sleep( 2 ) + job_state = self.__find_watched_job( job_id ) + if not job_state: + log.warn( "Failed to find job corresponding to final status %s in %s" % ( final_status, self.watched ) ) + else: + self.mark_as_finished( job_state ) + + def __find_watched_job( self, job_id ): + found_job = None + for async_job_state in self.watched: + if str( async_job_state.job_id ) == job_id: + found_job = async_job_state + break + return found_job + def queue_job(self, job_wrapper): job_destination = job_wrapper.job_destination @@ -184,15 +220,15 @@ return self.get_client( job_destination_params, job_id ) def get_client( self, job_destination_params, job_id ): - return self.client_manager.get_client( job_destination_params, job_id ) + return self.client_manager.get_client( job_destination_params, str( job_id ) ) def finish_job( self, job_state ): stderr = stdout = '' job_wrapper = job_state.job_wrapper try: client = self.get_client_from_state(job_state) + run_results = client.final_status() - run_results = client.raw_check_complete() stdout = run_results.get('stdout', '') stderr = run_results.get('stderr', '') exit_code = run_results.get('returncode', None) @@ -291,6 +327,10 @@ job_state.running = state == model.Job.states.RUNNING self.monitor_queue.put( job_state ) + def shutdown( self ): + super( LwrJobRunner, self ).shutdown() + self.client_manager.shutdown() + def __client_outputs( self, client, job_wrapper ): remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) if not remote_work_dir_copy: diff -r 7d649885e3259f3359e8c3816315c60e958c1518 -r 75b13d642f94b9ff6ec7c3c3713ad1177b243bd3 lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -8,6 +8,9 @@ from .setup_handler import build as build_setup_handler from .job_directory import RemoteJobDirectory +import logging +log = logging.getLogger(__name__) + CACHE_WAIT_SECONDS = 3 MAX_RETRY_COUNT = 5 RETRY_SLEEP_TIME = 0.1 @@ -272,6 +275,11 @@ launch_params["setup_params"] = dumps(setup_params) return self._raw_execute("launch", launch_params) + def final_status(self): + """ Return a dictionary summarizing final state of job. + """ + return self.raw_check_complete() + def kill(self): """ Cancel remote job, either removing from the queue or killing it. @@ -314,11 +322,11 @@ check_complete_response = self.raw_check_complete() # Older LWR instances won't set status so use 'complete', at some # point drop backward compatibility. - complete = self.check_complete(check_complete_response) - old_status = "complete" if complete else "running" - status = check_complete_response.get("status", old_status) + status = check_complete_response.get("status", None) # Bug in certains older LWR instances returned literal "status". - if status not in ["complete", "running", "queued"]: + if status in ["status", None]: + complete = self.check_complete(check_complete_response) + old_status = "complete" if complete else "running" status = old_status return status @@ -344,12 +352,12 @@ class MessageJobClient(BaseJobClient): - def __init__(self, destination_params, job_id, exchange): + def __init__(self, destination_params, job_id, client_manager): super(MessageJobClient, self).__init__(destination_params, job_id) if not self.job_directory: error_message = "Message-queue based LWR client requires destination define a remote job_directory to stage files into." raise Exception(error_message) - self.exchange = exchange + self.client_manager = client_manager def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): """ @@ -368,7 +376,19 @@ # before queueing. setup_params = _setup_params_from_job_config(job_config) launch_params["setup_params"] = setup_params - return self.exchange.publish("setup", launch_params) + return self.client_manager.exchange.publish("setup", launch_params) + + def clean(self): + del self.client_manager.final_status_cache[self.job_id] + + def final_status(self): + final_status = self.client_manager.final_status_cache.get(self.job_id, None) + if final_status is None: + raise Exception("final_status() called before a final status was properly cached with cilent manager.") + return final_status + + def kill(self): + log.warn("Kill not yet implemented with message queue driven LWR jobs.") class InputCachingJobClient(JobClient): diff -r 7d649885e3259f3359e8c3816315c60e958c1518 -r 75b13d642f94b9ff6ec7c3c3713ad1177b243bd3 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -1,9 +1,9 @@ from abc import ABCMeta, abstractmethod +import threading try: from Queue import Queue except ImportError: from queue import Queue -from threading import Thread from os import getenv try: from urllib import urlencode @@ -87,25 +87,35 @@ self.url = kwds.get('url') self.manager_name = kwds.get("manager", "_default_") self.exchange = LwrExchange(self.url, self.manager_name) - self.thread = None + self.final_status_cache = {} + self.callback_lock = threading.Lock() + self.callback_thread = None self.active = True - def listen_for_job_completes(self, callback): - # TODO: Call this from LWR runner. - def callback_wrapper(body, message): - callback(body) - message.ack() + def ensure_has_job_completes_callback(self, callback): + with self.callback_lock: + if self.callback_thread is not None: + return - def run(): - self.exchange.consume("complete", callback_wrapper, check=self) + def callback_wrapper(body, message): + try: + if "job_id" in body: + self.final_status_cache[body["job_id"]] = body + callback(body) + except Exception: + log.exception("Failure processing job status update message.") + message.ack() - t = Thread( - name="lwr_client_%s_complete_callback" % self.manager_name, - target=run - ) - t.daemon = False # Lets not interrupt processing of this. - t.start() - self.thread = t + def run(): + self.exchange.consume("complete", callback_wrapper, check=self) + + thread = threading.Thread( + name="lwr_client_%s_complete_callback" % self.manager_name, + target=run + ) + thread.daemon = False # Lets not interrupt processing of this. + thread.start() + self.callback_thread = thread def shutdown(self): self.active = False @@ -115,7 +125,7 @@ def get_client(self, destination_params, job_id): destination_params = _parse_destination_params(destination_params) - return MessageJobClient(destination_params, job_id, self.exchange) + return MessageJobClient(destination_params, job_id, self) class ObjectStoreClientManager(object): @@ -259,7 +269,7 @@ self.num_transfer_threads = num_transfer_threads self.transfer_queue = Queue() for i in range(num_transfer_threads): - t = Thread(target=self._transfer_worker) + t = threading.Thread(target=self._transfer_worker) t.daemon = True t.start() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: data libraries: visual tweaks, removal of buttons (now navigate through clicking on names)
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7d649885e325/ Changeset: 7d649885e325 User: martenson Date: 2014-02-17 23:17:36 Summary: data libraries: visual tweaks, removal of buttons (now navigate through clicking on names) Affected #: 5 files diff -r fb791568304883fe0357b6173dcc43d772214c8b -r 7d649885e3259f3359e8c3816315c60e958c1518 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -156,17 +156,17 @@ // FOLDER CONTENT tmpl_array.push('<table id="folder_table" class="table table-condensed">'); tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th class="button_heading">view</th>'); tmpl_array.push(' <th>name</th>'); tmpl_array.push(' <th>data type</th>'); tmpl_array.push(' <th>size</th>'); tmpl_array.push(' <th>date (UTC)</th>'); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); + tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' ..</td>'); tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); - tmpl_array.push(' <span class="fa fa-arrow-up"></span> .. go up</td>'); tmpl_array.push(' <td></td>'); tmpl_array.push(' <td></td>'); tmpl_array.push(' <td></td>'); @@ -175,9 +175,9 @@ tmpl_array.push(' <% _.each(items, function(content_item) { %>'); tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder + tmpl_array.push(' <td>'); + tmpl_array.push(' <span class="fa fa-folder-open"></span></td>'); tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">'); - tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>'); tmpl_array.push(' <td><%- content_item.get("name") %>'); tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder tmpl_array.push(' <span class="muted">(empty folder)</span>'); @@ -186,13 +186,11 @@ tmpl_array.push(' <td>folder</td>'); tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <span class="fa fa-file"></span>'); + tmpl_array.push(' </td>'); tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); - tmpl_array.push(' <td>'); - tmpl_array.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">'); - tmpl_array.push(' <span class="fa fa-eye"></span> details'); - tmpl_array.push(' </button>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <td><%- content_item.get("name") %></td>'); // dataset + tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>'); // dataset tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size tmpl_array.push(' <% } %> '); @@ -416,10 +414,16 @@ // prevent default event.preventDefault(); -//TODO check whether we already have the data + //TODO check whether we already have the data //load the ID of the row - var id = $(event.target).parent().parent().attr('id'); + var id = $(event.target).parent().parent().parent().attr('id'); + if (typeof id === 'undefined'){ + id = $(event.target).parent().attr('id'); + } + if (typeof id === 'undefined'){ + id = $(event.target).parent().parent().attr('id') + } //create new item var item = new Item(); @@ -430,7 +434,7 @@ //fetch the dataset info item.fetch({ success: function (item) { -// TODO can render here already + // TODO can render here already //fetch user histories for import purposes histories.fetch({ success: function (histories){ @@ -811,21 +815,16 @@ // tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); tmpl_array.push('<table class="table table-condensed">'); tmpl_array.push(' <thead>'); - tmpl_array.push(' <th class="button_heading"></th>'); tmpl_array.push(' <th>name</th>'); tmpl_array.push(' <th>description</th>'); tmpl_array.push(' <th>synopsis</th> '); - // tmpl_array.push(' <th>model type</th> '); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); tmpl_array.push(' <% _.each(libraries, function(library) { %>'); tmpl_array.push(' <tr>'); - tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">'); - tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>'); - tmpl_array.push(' <td><%- library.get("name") %></td>'); + tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>'); tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); - // tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% }); %>'); tmpl_array.push(' </tbody>'); @@ -862,7 +861,7 @@ that.$el.html(template); }, error: function(model, response){ - if (response.statusCode().status === 403){ + if (response.statusCode().status === 403){ //TODO open to public mod_toastr.info('Please log in first. Redirecting to login page in 3s.'); setTimeout(that.redirectToLogin, 3000); } else { diff -r fb791568304883fe0357b6173dcc43d772214c8b -r 7d649885e3259f3359e8c3816315c60e958c1518 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("/",{trigger:true,replace:false})}else{library_router.navigate("folders/"+r,{trigger:true,replace:false})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hide()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=Galaxy.modal;s.modal.show({closing_events:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hide()}}})},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hide();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hide();r.modal=null}}})},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hide();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hide()}}})},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hide();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th class="button_heading"></th>');r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(" ..</td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td>");r.push(' <span class="fa fa-folder-open"></span></td>');r.push(" <td></td>");r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(" <td>");r.push(' <span class="fa fa-file"></span>');r.push(" </td>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("/",{trigger:true,replace:false})}else{library_router.navigate("folders/"+r,{trigger:true,replace:false})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().parent().attr("id");if(typeof v==="undefined"){v=$(u.target).parent().attr("id")}if(typeof v==="undefined"){v=$(u.target).parent().parent().attr("id")}var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hide()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=Galaxy.modal;s.modal.show({closing_events:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hide()}}})},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hide();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hide();r.modal=null}}})},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hide();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hide()}}})},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hide();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file diff -r fb791568304883fe0357b6173dcc43d772214c8b -r 7d649885e3259f3359e8c3816315c60e958c1518 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1292,7 +1292,7 @@ tr.dark:hover td{background-color:#bbbfd0;color:white} a.dark:hover{color:yellow} a.dark{color:white} -th.button_heading{width:7em} +th.button_heading{width:2em} div.library_breadcrumb{padding-top:0.8em;padding-bottom:0.8em} div.library_breadcrumb a:hover{color:green} img.expanderIcon{padding-right:4px} diff -r fb791568304883fe0357b6173dcc43d772214c8b -r 7d649885e3259f3359e8c3816315c60e958c1518 static/style/blue/library.css --- a/static/style/blue/library.css +++ b/static/style/blue/library.css @@ -12,7 +12,7 @@ tr.dark:hover td{background-color:#bbbfd0;color:white} a.dark:hover{color:yellow} a.dark{color:white} -th.button_heading{width:7em} +th.button_heading{width:2em} div.library_breadcrumb{padding-top:0.8em;padding-bottom:0.8em} div.library_breadcrumb a:hover{color:green} img.expanderIcon{padding-right:4px} diff -r fb791568304883fe0357b6173dcc43d772214c8b -r 7d649885e3259f3359e8c3816315c60e958c1518 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -62,7 +62,7 @@ } th.button_heading { - width: 7em; + width: 2em; } div.library_breadcrumb{ padding-top: 0.8em; 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44968207ddd2/ Changeset: 44968207ddd2 Branch: stable User: carlfeberhard Date: 2014-02-17 22:20:21 Summary: Fix to history view: include purged datasets in history list when bootstrapping (this prevents them being added later and out of order when an update occurs) Affected #: 1 file diff -r fa8bdf1f6fc7318d120a3420c50e4045dbdb1e8b -r 44968207ddd283d0023c72e3d25fd39b1c71eb99 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -929,7 +929,9 @@ return trans.show_error_message( "Either you are not allowed to view this history" + " or the owner of this history has not made it accessible." ) - hdas = self.get_history_datasets( trans, history_to_view, show_deleted=True, show_hidden=True ) + # include all datasets: hidden, deleted, and purged + hdas = self.get_history_datasets( trans, history_to_view, + show_deleted=True, show_hidden=True, show_purged=True ) for hda in hdas: hda_dict = {} try: https://bitbucket.org/galaxy/galaxy-central/commits/fb7915683048/ Changeset: fb7915683048 User: carlfeberhard Date: 2014-02-17 22:20:42 Summary: Merge Affected #: 1 file diff -r 423a2939e224a294ded5842daa485da0a007fcbb -r fb791568304883fe0357b6173dcc43d772214c8b lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -900,7 +900,9 @@ return trans.show_error_message( "Either you are not allowed to view this history" + " or the owner of this history has not made it accessible." ) - hdas = self.get_history_datasets( trans, history_to_view, show_deleted=True, show_hidden=True ) + # include all datasets: hidden, deleted, and purged + hdas = self.get_history_datasets( trans, history_to_view, + show_deleted=True, show_hidden=True, show_purged=True ) for hda in hdas: hda_dict = {} try: 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.

1 0

commit/galaxy-central: jmchilton: Update LWR client through LWR changeset 5c609be.
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/423a2939e224/ Changeset: 423a2939e224 User: jmchilton Date: 2014-02-17 21:17:43 Summary: Update LWR client through LWR changeset 5c609be. The LWR server and client can be driven via message queues, though this changeset doesn't update the LWR runner itself to allow this - only the client itself. The runner however has been updated to support some more minor changes that enabled the LWR client to be message queue driven. In particular, a new action type was added "remote_copy" that does a file-system copy of files being staged in or out like "copy" - but it does so on the LWR side instead of the Galaxy client. In this scenario these actions are serialized and transferred with the "launch" command to the LWR - potentially eliminating many HTTP calls. Paired with this, more processing can happen on the client side - namely calculating remote paths and properties - and if configured in this fashion the LWR "setup" step can be eliminated - allowing the LWR client to completely specify a job with a single one-directional message (very useful for message queues). While modifying the LWR to be able to behave in this fashion was done to enable message queues - a traditional HTTP driven LWR can use these features (remote copy, client-side path calculation, etc...) and job_conf.xml.sample_advanced has been updated to reflect this. For more information on changes to the LWR client this encompasses see the following LWR changesets: https://bitbucket.org/jmchilton/lwr/commits/bacaa5c840bbf41952fcafe6e0deadd… https://bitbucket.org/jmchilton/lwr/commits/c8254d4525fa19f6761c6a75506d7b2… https://bitbucket.org/jmchilton/lwr/commits/1f068927a677bbfb932c475e5a4dad9… https://bitbucket.org/jmchilton/lwr/commits/bde8cbe6f5736a82d5fa20b322cb34d… https://bitbucket.org/jmchilton/lwr/commits/993910fa0c5a0ac2be72b2d70eeaaa0… Affected #: 14 files diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -96,6 +96,16 @@ ones (both alternatives are a little brittle). --> +  +  +  diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -6,19 +6,19 @@ from galaxy.jobs import JobDestination from galaxy.jobs.command_factory import build_command from galaxy.util import string_as_bool_or_none -from galaxy.util import in_directory from galaxy.util.bunch import Bunch import errno from time import sleep import os -from .lwr_client import ClientManager, url_to_destination_params +from .lwr_client import build_client_manager +from .lwr_client import url_to_destination_params from .lwr_client import finish_job as lwr_finish_job from .lwr_client import submit_job as lwr_submit_job from .lwr_client import ClientJobDescription from .lwr_client import LwrOutputs -from .lwr_client import GalaxyOutputs +from .lwr_client import ClientOutputs from .lwr_client import PathMapper log = logging.getLogger( __name__ ) @@ -41,7 +41,7 @@ self._init_monitor_thread() self._init_worker_threads() client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache)} - self.client_manager = ClientManager(**client_manager_kwargs) + self.client_manager = build_client_manager(**client_manager_kwargs) def url_to_destination( self, url ): """Convert a legacy URL to a job destination""" @@ -83,13 +83,12 @@ client_job_description = ClientJobDescription( command_line=command_line, - output_files=self.get_output_files(job_wrapper), input_files=self.get_input_files(job_wrapper), + client_outputs=self.__client_outputs(client, job_wrapper), working_directory=job_wrapper.working_directory, tool=job_wrapper.tool, config_files=job_wrapper.extra_filenames, requirements=requirements, - version_file=job_wrapper.get_version_string_path(), rewrite_paths=rewrite_paths, arbitrary_files=unstructured_path_rewrites, ) @@ -197,30 +196,17 @@ stdout = run_results.get('stdout', '') stderr = run_results.get('stderr', '') exit_code = run_results.get('returncode', None) - lwr_outputs = LwrOutputs(run_results) + lwr_outputs = LwrOutputs.from_status_response(run_results) # Use LWR client code to transfer/copy files back # and cleanup job if needed. completed_normally = \ job_wrapper.get_state() not in [ model.Job.states.ERROR, model.Job.states.DELETED ] cleanup_job = self.app.config.cleanup_job - remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) - if not remote_work_dir_copy: - work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) - else: - # They have already been copied over to look like regular outputs remotely, - # no need to handle them differently here. - work_dir_outputs = [] - output_files = self.get_output_files( job_wrapper ) - galaxy_outputs = GalaxyOutputs( - working_directory=job_wrapper.working_directory, - work_dir_outputs=work_dir_outputs, - output_files=output_files, - version_file=job_wrapper.get_version_string_path(), - ) + client_outputs = self.__client_outputs(client, job_wrapper) finish_args = dict( client=client, job_completed_normally=completed_normally, cleanup_job=cleanup_job, - galaxy_outputs=galaxy_outputs, + client_outputs=client_outputs, lwr_outputs=lwr_outputs ) failed = lwr_finish_job( **finish_args ) @@ -305,6 +291,23 @@ job_state.running = state == model.Job.states.RUNNING self.monitor_queue.put( job_state ) + def __client_outputs( self, client, job_wrapper ): + remote_work_dir_copy = LwrJobRunner.__remote_work_dir_copy( client ) + if not remote_work_dir_copy: + work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) + else: + # They have already been copied over to look like regular outputs remotely, + # no need to handle them differently here. + work_dir_outputs = [] + output_files = self.get_output_files( job_wrapper ) + client_outputs = ClientOutputs( + working_directory=job_wrapper.working_directory, + work_dir_outputs=work_dir_outputs, + output_files=output_files, + version_file=job_wrapper.get_version_string_path(), + ) + return client_outputs + @staticmethod def __dependency_resolution( lwr_client ): dependency_resolution = lwr_client.destination_params.get( "dependency_resolution", "local" ) diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/__init__.py @@ -10,20 +10,20 @@ from .staging.up import submit_job from .staging import ClientJobDescription from .staging import LwrOutputs -from .staging import GalaxyOutputs +from .staging import ClientOutputs from .client import OutputNotFoundException -from .manager import ClientManager +from .manager import build_client_manager from .destination import url_to_destination_params from .path_mapper import PathMapper __all__ = [ - ClientManager, + build_client_manager, OutputNotFoundException, url_to_destination_params, finish_job, submit_job, ClientJobDescription, LwrOutputs, - GalaxyOutputs, + ClientOutputs, PathMapper, ] diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/action_mapper.py --- a/lib/galaxy/jobs/runners/lwr_client/action_mapper.py +++ b/lib/galaxy/jobs/runners/lwr_client/action_mapper.py @@ -7,6 +7,7 @@ import fnmatch from re import compile from re import escape +import galaxy.util from galaxy.util.bunch import Bunch from .util import directory_files from .util import unique_path_prefix @@ -14,6 +15,11 @@ DEFAULT_MAPPED_ACTION = 'transfer' # Not really clear to me what this should be, exception? DEFAULT_PATH_MAPPER_TYPE = 'prefix' +STAGING_ACTION_REMOTE = "remote" +STAGING_ACTION_LOCAL = "local" +STAGING_ACTION_NONE = None +STAGING_ACTION_DEFAULT = "default" + # Poor man's enum. path_type = Bunch( # Galaxy input datasets and extra files. @@ -63,6 +69,7 @@ ... f.close() ... mock_client = Bunch(default_file_action=default_action, action_config_path=f.name) ... mapper = FileActionMapper(mock_client) + ... mapper = FileActionMapper(config=mapper.to_dict()) # Serialize and deserialize it to make sure still works ... unlink(f.name) ... return mapper >>> mapper = mapper_for(default_action='none', config_contents=json_string) @@ -110,18 +117,33 @@ True """ - def __init__(self, client): - self.default_action = client.default_file_action + def __init__(self, client=None, config=None): + if config is None and client is None: + message = "FileActionMapper must be constructed from either a client or a config dictionary." + raise Exception(message) + if config is None: + config = self.__client_to_config(client) + self.default_action = config.get("default_action", "transfer") + self.mappers = mappers_from_dicts(config.get("paths", [])) + + def to_dict(self): + return dict( + default_action=self.default_action, + paths=map(lambda m: m.to_dict(), self.mappers) + ) + + def __client_to_config(self, client): action_config_path = client.action_config_path - self.mappers = [] if action_config_path: - self.__load_action_config(action_config_path) + config = load(open(action_config_path, 'rb')) + else: + config = dict() + config["default_action"] = client.default_file_action + return config def __load_action_config(self, path): config = load(open(path, 'rb')) - for path_config in config.get('paths', []): - map_type = path_config.get('match_type', DEFAULT_PATH_MAPPER_TYPE) - self.mappers.append(mappers[map_type](path_config)) + self.mappers = mappers_from_dicts(config.get('paths', [])) def action(self, path, type, mapper=None): action_type = self.default_action if type in ACTION_DEFAULT_PATH_TYPES else "none" @@ -167,6 +189,14 @@ unstructured_map[path] = join(prefix, name) return unstructured_map + @property + def staging_needed(self): + return self.staging != STAGING_ACTION_NONE + + @property + def staging_action_local(self): + return self.staging == STAGING_ACTION_LOCAL + class NoneAction(BaseAction): """ This action indicates the corresponding path does not require any @@ -174,7 +204,7 @@ the LWR client (i.e. Galaxy server) and remote LWR server with the same paths. """ action_type = "none" - staging_needed = False + staging = STAGING_ACTION_NONE class TransferAction(BaseAction): @@ -182,7 +212,7 @@ transfer of the corresponding path to the remote LWR server before launching the job. """ action_type = "transfer" - staging_needed = True + staging = STAGING_ACTION_LOCAL class CopyAction(BaseAction): @@ -190,7 +220,74 @@ copy of the corresponding path to the LWR staging directory prior to launching the corresponding job. """ action_type = "copy" - staging_needed = True + staging = STAGING_ACTION_LOCAL + + +class RemoteCopyAction(BaseAction): + """ This action indicates the LWR server should copy the file before + execution via direct file system copy. This is like a CopyAction, but + it indicates the action should occur on the LWR server instead of on + the client. + """ + action_type = "remote_copy" + staging = STAGING_ACTION_REMOTE + + def to_dict(self): + return dict(path=self.path, action_type=RemoteCopyAction.action_type) + + @classmethod + def from_dict(cls, action_dict): + return RemoteCopyAction(path=action_dict["path"]) + + def write_to_path(self, path): + galaxy.util.copy_to_path(open(self.path, "rb"), path) + + +class MessageAction(object): + """ Sort of pseudo action describing "files" store in memory and + transferred via message (HTTP, Python-call, MQ, etc...) + """ + action_type = "message" + staging = STAGING_ACTION_DEFAULT + + def __init__(self, contents, client=None): + self.contents = contents + self.client = client + + @property + def staging_needed(self): + return True + + @property + def staging_action_local(self): + # Ekkk, cannot be called if created through from_dict. + # Shouldn't be a problem the way it is used - but is an + # object design problem. + return self.client.prefer_local_staging + + def to_dict(self): + return dict(contents=self.contents, action_type=MessageAction.action_type) + + @classmethod + def from_dict(cls, action_dict): + return MessageAction(contents=action_dict["contents"]) + + def write_to_path(self, path): + open(path, "w").write(self.contents) + +DICTIFIABLE_ACTION_CLASSES = [RemoteCopyAction, MessageAction] + + +def from_dict(action_dict): + action_type = action_dict.get("action_type", None) + target_class = None + for action_class in DICTIFIABLE_ACTION_CLASSES: + if action_type == action_class.action_type: + target_class = action_class + if not target_class: + message = "Failed to recover action from dictionary - invalid action type specified %s." % action_type + raise Exception(message) + return target_class.from_dict(action_dict) class BasePathMapper(object): @@ -207,8 +304,19 @@ path_type_matches = path_type in self.path_types return path_type_matches and self._path_matches(path) + def _extend_base_dict(self, **kwds): + base_dict = dict( + action=self.action_type, + path_types=",".join(self.path_types), + match_type=self.match_type, + **self.file_lister.to_dict() + ) + base_dict.update(**kwds) + return base_dict + class PrefixPathMapper(BasePathMapper): + match_type = 'prefix' def __init__(self, config): super(PrefixPathMapper, self).__init__(config) @@ -221,8 +329,12 @@ pattern_str = "(%s%s[^\s,\"\']+)" % (escape(self.prefix_path), escape(sep)) return compile(pattern_str) + def to_dict(self): + return self._extend_base_dict(path=self.prefix_path) + class GlobPathMapper(BasePathMapper): + match_type = 'glob' def __init__(self, config): super(GlobPathMapper, self).__init__(config) @@ -234,12 +346,17 @@ def to_pattern(self): return compile(fnmatch.translate(self.glob_path)) + def to_dict(self): + return self._extend_base_dict(path=self.glob_path) + class RegexPathMapper(BasePathMapper): + match_type = 'regex' def __init__(self, config): super(RegexPathMapper, self).__init__(config) - self.pattern = compile(config['path']) + self.pattern_raw = config['path'] + self.pattern = compile(self.pattern_raw) def _path_matches(self, path): return self.pattern.match(path) is not None @@ -247,12 +364,32 @@ def to_pattern(self): return self.pattern + def to_dict(self): + return self._extend_base_dict(path=self.pattern_raw) + +MAPPER_CLASSES = [PrefixPathMapper, GlobPathMapper, RegexPathMapper] +MAPPER_CLASS_DICT = dict(map(lambda c: (c.match_type, c), MAPPER_CLASSES)) + + +def mappers_from_dicts(mapper_def_list): + return map(lambda m: __mappper_from_dict(m), mapper_def_list) + + +def __mappper_from_dict(mapper_dict): + map_type = mapper_dict.get('match_type', DEFAULT_PATH_MAPPER_TYPE) + return MAPPER_CLASS_DICT[map_type](mapper_dict) + class FileLister(object): def __init__(self, config): self.depth = int(config.get("depth", "0")) + def to_dict(self): + return dict( + depth=self.depth + ) + def unstructured_map(self, path): depth = self.depth if self.depth == 0: @@ -265,14 +402,8 @@ DEFAULT_FILE_LISTER = FileLister(dict(depth=0)) -ACTION_CLASSES = [NoneAction, TransferAction, CopyAction] +ACTION_CLASSES = [NoneAction, TransferAction, CopyAction, RemoteCopyAction] actions = dict([(clazz.action_type, clazz) for clazz in ACTION_CLASSES]) -mappers = { - 'prefix': PrefixPathMapper, - 'glob': GlobPathMapper, - 'regex': RegexPathMapper, -} - -__all__ = [FileActionMapper, path_type] +__all__ = [FileActionMapper, path_type, from_dict, MessageAction] diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -0,0 +1,83 @@ +try: + import kombu + from kombu import pools +except ImportError: + kombu = None + +import socket +import logging +log = logging.getLogger(__name__) + + +KOMBU_UNAVAILABLE = "Attempting to bind to AMQP message queue, but kombu dependency unavailable" + +DEFAULT_EXCHANGE_NAME = "lwr" +DEFAULT_EXCHANGE_TYPE = "direct" +DEFAULT_TIMEOUT = 0.2 # Set timeout to periodically give up looking and check + # if polling should end. + + +class LwrExchange(object): + """ Utility for publishing and consuming structured LWR queues using kombu. + This is shared between the server and client - an exchange should be setup + for each manager (or in the case of the client, each manager one wished to + communicate with.) + + Each LWR manager is defined solely by name in the scheme, so only one LWR + should target each AMQP endpoint or care should be taken that unique + manager names are used across LWR servers targetting same AMQP endpoint - + and in particular only one such LWR should define an default manager with + name _default_. + """ + + def __init__(self, url, manager_name, timeout=DEFAULT_TIMEOUT): + """ + """ + if not kombu: + raise Exception(KOMBU_UNAVAILABLE) + self.__url = url + self.__manager_name = manager_name + self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) + self.__timeout = timeout + + def consume(self, queue_name, callback, check=True, connection_kwargs={}): + queue = self.__queue(queue_name) + with self.connection(self.__url, **connection_kwargs) as connection: + with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): + while check: + try: + connection.drain_events(timeout=self.__timeout) + except socket.timeout: + pass + + def publish(self, name, payload): + with self.connection(self.__url) as connection: + with pools.producers[connection].acquire() as producer: + key = self.__queue_name(name) + producer.publish( + payload, + serializer='json', + exchange=self.__exchange, + declare=[self.__exchange], + routing_key=key, + ) + + def connection(self, connection_string, **kwargs): + return kombu.Connection(connection_string, **kwargs) + + def __queue(self, name): + queue_name = self.__queue_name(name) + queue = kombu.Queue(queue_name, self.__exchange, routing_key=queue_name) + return queue + + def __queue_name(self, name): + key_prefix = self.__key_prefix() + queue_name = '%s_%s' % (key_prefix, name) + return queue_name + + def __key_prefix(self): + if self.__manager_name == "_default_": + key_prefix = "lwr_" + else: + key_prefix = "lwr_%s_" % self.__manager_name + return key_prefix diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/client.py --- a/lib/galaxy/jobs/runners/lwr_client/client.py +++ b/lib/galaxy/jobs/runners/lwr_client/client.py @@ -1,9 +1,12 @@ import os import shutil -from json import dumps, loads +import json +from json import dumps from time import sleep from .destination import submit_params +from .setup_handler import build as build_setup_handler +from .job_directory import RemoteJobDirectory CACHE_WAIT_SECONDS = 3 MAX_RETRY_COUNT = 5 @@ -15,7 +18,7 @@ def __call__(self, func): def replacement(*args, **kwargs): response = func(*args, **kwargs) - return loads(response) + return json.loads(response) return replacement @@ -49,7 +52,47 @@ return "No remote output found for path %s" % self.path -class JobClient(object): +class BaseJobClient(object): + + def __init__(self, destination_params, job_id): + self.destination_params = destination_params + self.job_id = job_id + if "jobs_directory" in (destination_params or {}): + staging_directory = destination_params["jobs_directory"] + sep = destination_params.get("remote_sep", os.sep) + job_directory = RemoteJobDirectory( + remote_staging_directory=staging_directory, + remote_id=job_id, + remote_sep=sep, + ) + else: + job_directory = None + self.job_directory = job_directory + + self.default_file_action = self.destination_params.get("default_file_action", "transfer") + self.action_config_path = self.destination_params.get("file_action_config", None) + + self.setup_handler = build_setup_handler(self, destination_params) + + def setup(self, tool_id=None, tool_version=None): + """ + Setup remote LWR server to run this job. + """ + setup_args = {"job_id": self.job_id} + if tool_id: + setup_args["tool_id"] = tool_id + if tool_version: + setup_args["tool_version"] = tool_version + return self.setup_handler.setup(**setup_args) + + @property + def prefer_local_staging(self): + # If doing a job directory is defined, calculate paths here and stage + # remotely. + return self.job_directory is None + + +class JobClient(BaseJobClient): """ Objects of this client class perform low-level communication with a remote LWR server. @@ -62,12 +105,8 @@ """ def __init__(self, destination_params, job_id, job_manager_interface): + super(JobClient, self).__init__(destination_params, job_id) self.job_manager_interface = job_manager_interface - self.destination_params = destination_params - self.job_id = job_id - - self.default_file_action = self.destination_params.get("default_file_action", "transfer") - self.action_config_path = self.destination_params.get("file_action_config", None) def _raw_execute(self, command, args={}, data=None, input_path=None, output_path=None): return self.job_manager_interface.execute(command, args, data, input_path, output_path) @@ -206,10 +245,11 @@ } self._raw_execute("download_output", output_params, output_path=output_path) - def launch(self, command_line, requirements=[]): + def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): """ - Run or queue up the execution of the supplied - `command_line` on the remote server. + Queue up the execution of the supplied `command_line` on the remote + server. Called launch for historical reasons, should be renamed to + enqueue or something like that. **Parameters** @@ -222,6 +262,14 @@ launch_params['params'] = dumps(submit_params) if requirements: launch_params['requirements'] = dumps([requirement.to_dict() for requirement in requirements]) + if remote_staging: + launch_params['remote_staging'] = dumps(remote_staging) + if job_config and self.setup_handler.local: + # Setup not yet called, job properties were inferred from + # destination arguments. Hence, must have LWR setup job + # before queueing. + setup_params = _setup_params_from_job_config(job_config) + launch_params["setup_params"] = dumps(setup_params) return self._raw_execute("launch", launch_params) def kill(self): @@ -230,15 +278,20 @@ """ return self._raw_execute("kill", {"job_id": self.job_id}) - def wait(self): + def wait(self, max_seconds=None): """ Wait for job to finish. """ - while True: + i = 0 + while max_seconds is None or i < max_seconds: complete_response = self.raw_check_complete() if complete_response["complete"] == "true": + print complete_response return complete_response + else: + print complete_response sleep(1) + i += 1 @parseJson() def raw_check_complete(self): @@ -276,15 +329,10 @@ self._raw_execute("clean", {"job_id": self.job_id}) @parseJson() - def setup(self, tool_id=None, tool_version=None): + def remote_setup(self, **setup_args): """ Setup remote LWR server to run this job. """ - setup_args = {"job_id": self.job_id} - if tool_id: - setup_args["tool_id"] = tool_id - if tool_version: - setup_args["tool_version"] = tool_version return self._raw_execute("setup", setup_args) def _copy(self, source, destination): @@ -294,6 +342,35 @@ shutil.copyfile(source, destination) +class MessageJobClient(BaseJobClient): + + def __init__(self, destination_params, job_id, exchange): + super(MessageJobClient, self).__init__(destination_params, job_id) + if not self.job_directory: + error_message = "Message-queue based LWR client requires destination define a remote job_directory to stage files into." + raise Exception(error_message) + self.exchange = exchange + + def launch(self, command_line, requirements=[], remote_staging=[], job_config=None): + """ + """ + launch_params = dict(command_line=command_line, job_id=self.job_id) + submit_params_dict = submit_params(self.destination_params) + if submit_params_dict: + launch_params['params'] = submit_params_dict + if requirements: + launch_params['requirements'] = [requirement.to_dict() for requirement in requirements] + if remote_staging: + launch_params['remote_staging'] = remote_staging + if job_config and self.setup_handler.local: + # Setup not yet called, job properties were inferred from + # destination arguments. Hence, must have LWR setup job + # before queueing. + setup_params = _setup_params_from_job_config(job_config) + launch_params["setup_params"] = setup_params + return self.exchange.publish("setup", launch_params) + + class InputCachingJobClient(JobClient): """ Beta client that cache's staged files to prevent duplication. @@ -337,6 +414,17 @@ return self._raw_execute("file_available", {"path": path}) +def _setup_params_from_job_config(job_config): + job_id = job_config.get("job_id", None) + tool_id = job_config.get("tool_id", None) + tool_version = job_config.get("tool_version", None) + return dict( + job_id=job_id, + tool_id=tool_id, + tool_version=tool_version + ) + + class ObjectStoreClient(object): def __init__(self, lwr_interface): diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/destination.py --- a/lib/galaxy/jobs/runners/lwr_client/destination.py +++ b/lib/galaxy/jobs/runners/lwr_client/destination.py @@ -1,5 +1,6 @@ from re import match +from .util import filter_destination_params SUBMIT_PREFIX = "submit_" @@ -54,7 +55,4 @@ >>> result {'native_specification': '-q batch'} """ - destination_params = destination_params or {} - return dict([(key[len(SUBMIT_PREFIX):], destination_params[key]) - for key in destination_params - if key.startswith(SUBMIT_PREFIX)]) + return filter_destination_params(destination_params, SUBMIT_PREFIX) diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/job_directory.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/job_directory.py @@ -0,0 +1,137 @@ +""" +""" +import os.path +from collections import deque +import posixpath + +from .util import PathHelper +from galaxy.util import in_directory + +from logging import getLogger +log = getLogger(__name__) + + +TYPES_TO_METHOD = dict( + input="inputs_directory", + input_extra="inputs_directory", + unstructured="unstructured_files_directory", + config="configs_directory", + tool="tool_files_directory", + work_dir="working_directory", + workdir="working_directory", + output="outputs_directory", + output_workdir="working_directory", +) + + +class RemoteJobDirectory(object): + """ Representation of a (potentially) remote LWR-style staging directory. + """ + + def __init__(self, remote_staging_directory, remote_id, remote_sep): + self.path_helper = PathHelper(remote_sep) + self.job_directory = self.path_helper.remote_join( + remote_staging_directory, + remote_id + ) + + def working_directory(self): + return self._sub_dir('working') + + def inputs_directory(self): + return self._sub_dir('inputs') + + def outputs_directory(self): + return self._sub_dir('outputs') + + def configs_directory(self): + return self._sub_dir('configs') + + def tool_files_directory(self): + return self._sub_dir('tool_files') + + def unstructured_files_directory(self): + return self._sub_dir('unstructured') + + @property + def path(self): + return self.job_directory + + @property + def separator(self): + return self.path_helper.separator + + def calculate_path(self, remote_relative_path, input_type): + """ Only for used by LWR client, should override for managers to + enforce security and make the directory if needed. + """ + directory, allow_nested_files = self._directory_for_file_type(input_type) + return self.path_helper.remote_join(directory, remote_relative_path) + + def _directory_for_file_type(self, file_type): + allow_nested_files = False + # work_dir and input_extra are types used by legacy clients... + # Obviously this client won't be legacy because this is in the + # client module, but this code is reused on server which may + # serve legacy clients. + allow_nested_files = file_type in ['input', 'input_extra', 'unstructured', 'output', 'output_workdir'] + directory_function = getattr(self, TYPES_TO_METHOD.get(file_type, None), None) + if not directory_function: + raise Exception("Unknown file_type specified %s" % file_type) + return directory_function(), allow_nested_files + + def _sub_dir(self, name): + return self.path_helper.remote_join(self.job_directory, name) + + +def get_mapped_file(directory, remote_path, allow_nested_files=False, local_path_module=os.path, mkdir=True): + """ + + >>> import ntpath + >>> get_mapped_file(r'C:\\lwr\\staging\\101', 'dataset_1_files/moo/cow', allow_nested_files=True, local_path_module=ntpath, mkdir=False) + 'C:\\\\lwr\\\\staging\\\\101\\\\dataset_1_files\\\\moo\\\\cow' + >>> get_mapped_file(r'C:\\lwr\\staging\\101', 'dataset_1_files/moo/cow', allow_nested_files=False, local_path_module=ntpath) + 'C:\\\\lwr\\\\staging\\\\101\\\\cow' + >>> get_mapped_file(r'C:\\lwr\\staging\\101', '../cow', allow_nested_files=True, local_path_module=ntpath, mkdir=False) + Traceback (most recent call last): + Exception: Attempt to read or write file outside an authorized directory. + """ + if not allow_nested_files: + name = local_path_module.basename(remote_path) + path = local_path_module.join(directory, name) + else: + local_rel_path = __posix_to_local_path(remote_path, local_path_module=local_path_module) + local_path = local_path_module.join(directory, local_rel_path) + verify_is_in_directory(local_path, directory, local_path_module=local_path_module) + local_directory = local_path_module.dirname(local_path) + if mkdir and not local_path_module.exists(local_directory): + os.makedirs(local_directory) + path = local_path + return path + + +def __posix_to_local_path(path, local_path_module=os.path): + """ + Converts a posix path (coming from Galaxy), to a local path (be it posix or Windows). + + >>> import ntpath + >>> __posix_to_local_path('dataset_1_files/moo/cow', local_path_module=ntpath) + 'dataset_1_files\\\\moo\\\\cow' + >>> import posixpath + >>> __posix_to_local_path('dataset_1_files/moo/cow', local_path_module=posixpath) + 'dataset_1_files/moo/cow' + """ + partial_path = deque() + while True: + if not path or path == '/': + break + (path, base) = posixpath.split(path) + partial_path.appendleft(base) + return local_path_module.join(*partial_path) + + +def verify_is_in_directory(path, directory, local_path_module=os.path): + if not in_directory(path, directory, local_path_module): + msg = "Attempt to read or write file outside an authorized directory." + log.warn("%s Attempted path: %s, valid directory: %s" % (msg, path, directory)) + raise Exception(msg) diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -21,9 +21,11 @@ from .client import JobClient from .client import InputCachingJobClient from .client import ObjectStoreClient +from .client import MessageJobClient from .transport import get_transport from .util import TransferEventManager from .destination import url_to_destination_params +from .amqp_exchange import LwrExchange from logging import getLogger @@ -32,6 +34,15 @@ DEFAULT_TRANSFER_THREADS = 2 +def build_client_manager(**kwargs): + if 'job_manager' in kwargs: + return ClientManager(**kwargs) # TODO: Consider more separation here. + elif 'url' in kwargs: + return MessageQueueClientManager(**kwargs) + else: + return ClientManager(**kwargs) + + class ClientManager(object): """ Factory to create LWR clients, used to manage potential shared @@ -60,20 +71,51 @@ self.extra_client_kwds = {} def get_client(self, destination_params, job_id): - destination_params = self.__parse_destination_params(destination_params) + destination_params = _parse_destination_params(destination_params) job_manager_interface_class = self.job_manager_interface_class job_manager_interface_args = dict(destination_params=destination_params, **self.job_manager_interface_args) job_manager_interface = job_manager_interface_class(**job_manager_interface_args) return self.client_class(destination_params, job_id, job_manager_interface, **self.extra_client_kwds) - def __parse_destination_params(self, destination_params): - try: - unicode_type = unicode - except NameError: - unicode_type = str - if isinstance(destination_params, str) or isinstance(destination_params, unicode_type): - destination_params = url_to_destination_params(destination_params) - return destination_params + def shutdown(self): + pass + + +class MessageQueueClientManager(object): + + def __init__(self, **kwds): + self.url = kwds.get('url') + self.manager_name = kwds.get("manager", "_default_") + self.exchange = LwrExchange(self.url, self.manager_name) + self.thread = None + self.active = True + + def listen_for_job_completes(self, callback): + # TODO: Call this from LWR runner. + def callback_wrapper(body, message): + callback(body) + message.ack() + + def run(): + self.exchange.consume("complete", callback_wrapper, check=self) + + t = Thread( + name="lwr_client_%s_complete_callback" % self.manager_name, + target=run + ) + t.daemon = False # Lets not interrupt processing of this. + t.start() + self.thread = t + + def shutdown(self): + self.active = False + + def __nonzero__(self): + return self.active + + def get_client(self, destination_params, job_id): + destination_params = _parse_destination_params(destination_params) + return MessageJobClient(destination_params, job_id, self.exchange) class ObjectStoreClientManager(object): @@ -163,7 +205,8 @@ if controller.response_type != 'file': return controller.body(result) else: - from lwr.util import copy_to_path + # TODO: Add to Galaxy. + from galaxy.util import copy_to_path with open(result, 'rb') as result_file: copy_to_path(result_file, output_path) @@ -221,6 +264,16 @@ t.start() +def _parse_destination_params(destination_params): + try: + unicode_type = unicode + except NameError: + unicode_type = str + if isinstance(destination_params, str) or isinstance(destination_params, unicode_type): + destination_params = url_to_destination_params(destination_params) + return destination_params + + def _environ_default_int(variable, default="0"): val = getenv(variable, default) int_val = int(default) diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/setup_handler.py --- /dev/null +++ b/lib/galaxy/jobs/runners/lwr_client/setup_handler.py @@ -0,0 +1,103 @@ +import os +from .util import filter_destination_params + +REMOTE_SYSTEM_PROPERTY_PREFIX = "remote_property_" + + +def build(client, destination_args): + """ Build a SetupHandler object for client from destination parameters. + """ + # Have defined a remote job directory, lets do the setup locally. + if client.job_directory: + handler = LocalSetupHandler(client, destination_args) + else: + handler = RemoteSetupHandler(client) + return handler + + +class LocalSetupHandler(object): + """ Parse destination params to infer job setup parameters (input/output + directories, etc...). Default is to get this configuration data from the + remote LWR server. + + Downside of this approach is that it requires more and more dependent + configuraiton of Galaxy. Upside is that it is asynchronous and thus makes + message queue driven configurations possible. + + Remote system properties (such as galaxy_home) can be specified in + destination args by prefixing property with remote_property_ (e.g. + remote_property_galaxy_home). + """ + + def __init__(self, client, destination_args): + self.client = client + system_properties = self.__build_system_properties(destination_args) + system_properties["sep"] = client.job_directory.separator + self.system_properties = system_properties + self.jobs_directory = destination_args["jobs_directory"] + + def setup(self, job_id, tool_id=None, tool_version=None): + return build_job_config( + job_id=job_id, + job_directory=self.client.job_directory, + system_properties=self.system_properties, + tool_id=tool_id, + tool_version=tool_version, + ) + + @property + def local(self): + """ + """ + return True + + def __build_system_properties(self, destination_params): + return filter_destination_params(destination_params, REMOTE_SYSTEM_PROPERTY_PREFIX) + + +class RemoteSetupHandler(object): + """ Default behavior. Fetch setup information from remote LWR server. + """ + def __init__(self, client): + self.client = client + + def setup(self, **setup_args): + return self.client.remote_setup(**setup_args) + + @property + def local(self): + """ + """ + return False + + +def build_job_config(job_id, job_directory, system_properties={}, tool_id=None, tool_version=None): + """ + """ + inputs_directory = job_directory.inputs_directory() + working_directory = job_directory.working_directory() + outputs_directory = job_directory.outputs_directory() + configs_directory = job_directory.configs_directory() + tools_directory = job_directory.tool_files_directory() + unstructured_files_directory = job_directory.unstructured_files_directory() + sep = system_properties.get("sep", os.sep) + job_config = { + "working_directory": working_directory, + "outputs_directory": outputs_directory, + "configs_directory": configs_directory, + "tools_directory": tools_directory, + "inputs_directory": inputs_directory, + "unstructured_files_directory": unstructured_files_directory, + # Poorly named legacy attribute. Drop at some point. + "path_separator": sep, + "job_id": job_id, + "system_properties": system_properties, + } + if tool_id: + job_config["tool_id"] = tool_id + if tool_version: + job_config["tool_version"] = tool_version + return job_config + + +__all__ = [build_job_config, build] diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/staging/__init__.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/__init__.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/__init__.py @@ -14,15 +14,20 @@ **Parameters** command_line : str - The local command line to execute, this will be rewritten for the remote server. + The local command line to execute, this will be rewritten for + the remote server. config_files : list - List of Galaxy 'configfile's produced for this job. These will be rewritten and sent to remote server. + List of Galaxy 'configfile's produced for this job. These will + be rewritten and sent to remote server. input_files : list - List of input files used by job. These will be transferred and references rewritten. - output_files : list - List of output_files produced by job. + List of input files used by job. These will be transferred and + references rewritten. + client_outputs : ClientOutputs + Description of outputs produced by job (at least output files along + with optional version string and working directory outputs. tool_dir : str - Directory containing tool to execute (if a wrapper is used, it will be transferred to remote server). + Directory containing tool to execute (if a wrapper is used, it will + be transferred to remote server). working_directory : str Local path created by Galaxy for running this job. requirements : list @@ -46,10 +51,9 @@ command_line, config_files, input_files, - output_files, + client_outputs, working_directory, requirements, - version_file=None, arbitrary_files=None, rewrite_paths=True, ): @@ -57,38 +61,74 @@ self.command_line = command_line self.config_files = config_files self.input_files = input_files - self.output_files = output_files + self.client_outputs = client_outputs self.working_directory = working_directory self.requirements = requirements - self.version_file = version_file self.rewrite_paths = rewrite_paths self.arbitrary_files = arbitrary_files or {} + @property + def output_files(self): + return self.client_outputs.output_files -class GalaxyOutputs(object): + @property + def version_file(self): + return self.client_outputs.version_file + + +class ClientOutputs(object): """ Abstraction describing the output datasets EXPECTED by the Galaxy job - runner client. """ + runner client. + """ - def __init__(self, working_directory, work_dir_outputs, output_files, version_file): + def __init__(self, working_directory, output_files, work_dir_outputs=None, version_file=None): self.working_directory = working_directory self.work_dir_outputs = work_dir_outputs self.output_files = output_files self.version_file = version_file + def to_dict(self): + return dict( + working_directory=self.working_directory, + work_dir_outputs=self.work_dir_outputs, + output_files=self.output_files, + version_file=self.version_file + ) + + @staticmethod + def from_dict(config_dict): + return ClientOutputs( + working_directory=config_dict.get('working_directory'), + work_dir_outputs=config_dict.get('work_dir_outputs'), + output_files=config_dict.get('output_files'), + version_file=config_dict.get('version_file'), + ) + class LwrOutputs(object): """ Abstraction describing the output files PRODUCED by the remote LWR server. """ - def __init__(self, complete_response): + def __init__(self, working_directory_contents, output_directory_contents, remote_separator=sep): + self.working_directory_contents = working_directory_contents + self.output_directory_contents = output_directory_contents + self.path_helper = PathHelper(remote_separator) + + @staticmethod + def from_status_response(complete_response): # Default to None instead of [] to distinguish between empty contents and it not set # by the LWR - older LWR instances will not set these in complete response. - self.working_directory_contents = complete_response.get("working_directory_contents", None) - self.output_directory_contents = complete_response.get("outputs_directory_contents", None) + working_directory_contents = complete_response.get("working_directory_contents", None) + output_directory_contents = complete_response.get("outputs_directory_contents", None) # Older (pre-2014) LWR servers will not include separator in response, - #so this should only be used when reasoning about outputs in - # subdirectories which was not previously supported. - self.path_helper = PathHelper(complete_response.get("system_properties", {}).get("separator", sep)) + # so this should only be used when reasoning about outputs in + # subdirectories (which was not previously supported prior to that). + remote_separator = complete_response.get("system_properties", {}).get("separator", sep) + return LwrOutputs( + working_directory_contents, + output_directory_contents, + remote_separator + ) def has_output_file(self, output_file): if self.output_directory_contents is None: diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/staging/down.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/down.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/down.py @@ -17,111 +17,144 @@ COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+\.dat|dataset_\d+_files.+") -def finish_job(client, cleanup_job, job_completed_normally, galaxy_outputs, lwr_outputs): +def finish_job(client, cleanup_job, job_completed_normally, client_outputs, lwr_outputs): """ Responsible for downloading results from remote server and cleaning up LWR staging directory (if needed.) """ - download_failure_exceptions = [] + collection_failure_exceptions = [] if job_completed_normally: - downloader = ResultsDownloader(client, galaxy_outputs, lwr_outputs) - download_failure_exceptions = downloader.download() - return __clean(download_failure_exceptions, cleanup_job, client) + output_collector = ClientOutputCollector(client) + action_mapper = FileActionMapper(client) + results_stager = ResultsCollector(output_collector, action_mapper, client_outputs, lwr_outputs) + collection_failure_exceptions = results_stager.collect() + __clean(collection_failure_exceptions, cleanup_job, client) + return collection_failure_exceptions -class ResultsDownloader(object): +class ClientOutputCollector(object): - def __init__(self, client, galaxy_outputs, lwr_outputs): + def __init__(self, client): self.client = client - self.galaxy_outputs = galaxy_outputs + + def collect_output(self, results_collector, output_type, action, name): + # This output should have been handled by the LWR. + if not action.staging_action_local: + return False + + path = action.path + if output_type == 'legacy': + working_directory = results_collector.client_outputs.working_directory + self.client.fetch_output_legacy(path, working_directory, action_type=action.action_type) + elif output_type == 'output_workdir': + working_directory = results_collector.client_outputs.working_directory + self.client.fetch_work_dir_output(name, working_directory, path, action_type=action.action_type) + elif output_type == 'output': + self.client.fetch_output(path=path, name=name, action_type=action.action_type) + return True + + +class ResultsCollector(object): + + def __init__(self, output_collector, action_mapper, client_outputs, lwr_outputs): + self.output_collector = output_collector + self.action_mapper = action_mapper + self.client_outputs = client_outputs self.lwr_outputs = lwr_outputs - self.action_mapper = FileActionMapper(client) self.downloaded_working_directory_files = [] self.exception_tracker = DownloadExceptionTracker() - self.output_files = galaxy_outputs.output_files + self.output_files = client_outputs.output_files self.working_directory_contents = lwr_outputs.working_directory_contents or [] - def download(self): - self.__download_working_directory_outputs() - self.__download_outputs() - self.__download_version_file() - self.__download_other_working_directory_files() - return self.exception_tracker.download_failure_exceptions + def collect(self): + self.__collect_working_directory_outputs() + self.__collect_outputs() + self.__collect_version_file() + self.__collect_other_working_directory_files() + return self.exception_tracker.collection_failure_exceptions - def __download_working_directory_outputs(self): - working_directory = self.galaxy_outputs.working_directory + def __collect_working_directory_outputs(self): + working_directory = self.client_outputs.working_directory # Fetch explicit working directory outputs. - for source_file, output_file in self.galaxy_outputs.work_dir_outputs: + for source_file, output_file in self.client_outputs.work_dir_outputs: name = relpath(source_file, working_directory) - remote_name = self.lwr_outputs.path_helper.remote_name(name) - with self.exception_tracker(): - action = self.action_mapper.action(output_file, 'output_workdir') - self.client.fetch_work_dir_output(remote_name, working_directory, output_file, action_type=action.action_type) - self.downloaded_working_directory_files.append(remote_name) + lwr_name = self.lwr_outputs.path_helper.remote_name(name) + if self._attempt_collect_output('output_workdir', path=output_file, name=lwr_name): + self.downloaded_working_directory_files.append(lwr_name) # Remove from full output_files list so don't try to download directly. self.output_files.remove(output_file) - def __download_outputs(self): + def __collect_outputs(self): # Legacy LWR not returning list of files, iterate over the list of # expected outputs for tool. for output_file in self.output_files: - # Fetch ouptut directly... - with self.exception_tracker(): - action = self.action_mapper.action(output_file, 'output') - output_generated = self.lwr_outputs.has_output_file(output_file) - working_directory = self.galaxy_outputs.working_directory - if output_generated is None: - self.client.fetch_output_legacy(output_file, working_directory, action_type=action.action_type) - elif output_generated: - self.client.fetch_output(output_file, action_type=action.action_type) + # Fetch output directly... + output_generated = self.lwr_outputs.has_output_file(output_file) + if output_generated is None: + self._attempt_collect_output('legacy', output_file) + elif output_generated: + self._attempt_collect_output('output', output_file) - for local_path, remote_name in self.lwr_outputs.output_extras(output_file).iteritems(): - with self.exception_tracker(): - action = self.action_mapper.action(local_path, 'output') - self.client.fetch_output(path=local_path, name=remote_name, action_type=action.action_type) + for galaxy_path, lwr_name in self.lwr_outputs.output_extras(output_file).iteritems(): + self._attempt_collect_output('output', path=galaxy_path, name=lwr_name) # else not output generated, do not attempt download. - def __download_version_file(self): - version_file = self.galaxy_outputs.version_file + def __collect_version_file(self): + version_file = self.client_outputs.version_file # output_directory_contents may be none for legacy LWR servers. lwr_output_directory_contents = (self.lwr_outputs.output_directory_contents or []) if version_file and COMMAND_VERSION_FILENAME in lwr_output_directory_contents: - action = self.action_mapper.action(version_file, 'output') - self.client.fetch_output(path=version_file, name=COMMAND_VERSION_FILENAME, action_type=action.action_type) + self._attempt_collect_output('output', version_file, name=COMMAND_VERSION_FILENAME) - def __download_other_working_directory_files(self): - working_directory = self.galaxy_outputs.working_directory + def __collect_other_working_directory_files(self): + working_directory = self.client_outputs.working_directory # Fetch remaining working directory outputs of interest. for name in self.working_directory_contents: if name in self.downloaded_working_directory_files: continue if COPY_FROM_WORKING_DIRECTORY_PATTERN.match(name): - with self.exception_tracker(): - output_file = join(working_directory, self.lwr_outputs.path_helper.local_name(name)) - action = self.action_mapper.action(output_file, 'output_workdir') - self.client.fetch_work_dir_output(name, working_directory, output_file, action_type=action.action_type) + output_file = join(working_directory, self.lwr_outputs.path_helper.local_name(name)) + if self._attempt_collect_output(output_type='output_workdir', path=output_file, name=name): self.downloaded_working_directory_files.append(name) + def _attempt_collect_output(self, output_type, path, name=None): + # path is final path on galaxy server (client) + # name is the 'name' of the file on the LWR server (possible a relative) + # path. + collected = False + with self.exception_tracker(): + # output_action_type cannot be 'legacy' but output_type may be + # eventually drop support for legacy mode (where type wasn't known) + # ahead of time. + output_action_type = 'output_workdir' if output_type == 'output_workdir' else 'output' + action = self.action_mapper.action(path, output_action_type) + if self._collect_output(output_type, action, name): + collected = True + + return collected + + def _collect_output(self, output_type, action, name): + return self.output_collector.collect_output(self, output_type, action, name) + class DownloadExceptionTracker(object): def __init__(self): - self.download_failure_exceptions = [] + self.collection_failure_exceptions = [] @contextmanager def __call__(self): try: yield except Exception as e: - self.download_failure_exceptions.append(e) + self.collection_failure_exceptions.append(e) -def __clean(download_failure_exceptions, cleanup_job, client): - failed = (len(download_failure_exceptions) > 0) +def __clean(collection_failure_exceptions, cleanup_job, client): + failed = (len(collection_failure_exceptions) > 0) if (not failed and cleanup_job != "never") or cleanup_job == "always": try: client.clean() - except: + except Exception: log.warn("Failed to cleanup remote LWR job") - return failed __all__ = [finish_job] diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/staging/up.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/up.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/up.py @@ -8,6 +8,7 @@ from ..staging import COMMAND_VERSION_FILENAME from ..action_mapper import FileActionMapper from ..action_mapper import path_type +from ..action_mapper import MessageAction from ..util import PathHelper from ..util import directory_files @@ -21,7 +22,24 @@ file_stager = FileStager(client, client_job_description, job_config) rebuilt_command_line = file_stager.get_command_line() job_id = file_stager.job_id - client.launch(rebuilt_command_line, requirements=client_job_description.requirements) + launch_kwds = dict( + command_line=rebuilt_command_line, + requirements=client_job_description.requirements, + ) + if file_stager.job_config: + launch_kwds["job_config"] = file_stager.job_config + remote_staging = {} + remote_staging_actions = file_stager.transfer_tracker.remote_staging_actions + if remote_staging_actions: + remote_staging["setup"] = remote_staging_actions + # Somehow make the following optional. + remote_staging["action_mapper"] = file_stager.action_mapper.to_dict() + remote_staging["client_outputs"] = client_job_description.client_outputs.to_dict() + + if remote_staging: + launch_kwds["remote_staging"] = remote_staging + + client.launch(**launch_kwds) return job_id @@ -100,6 +118,7 @@ # Remote LWR server assigned an id different than the # Galaxy job id, update client to reflect this. self.client.job_id = self.job_id + self.job_config = job_config def __parse_remote_separator(self, job_config): separator = job_config.get("system_properties", {}).get("separator", None) @@ -195,7 +214,7 @@ def __upload_rewritten_config_files(self): for config_file, new_config_contents in self.job_inputs.config_files.items(): - self.client.put_file(config_file, input_type='config', contents=new_config_contents) + self.transfer_tracker.handle_transfer(config_file, type='config', contents=new_config_contents) def get_command_line(self): """ @@ -317,29 +336,48 @@ self.job_inputs = job_inputs self.rewrite_paths = rewrite_paths self.file_renames = {} + self.remote_staging_actions = [] def handle_transfer(self, path, type, name=None, contents=None): + action = self.__action_for_transfer(path, type, contents) + + if action.staging_needed: + local_action = action.staging_action_local + if local_action: + response = self.client.put_file(path, type, name=name, contents=contents) + get_path = lambda: response['path'] + else: + job_directory = self.client.job_directory + assert job_directory, "job directory required for action %s" % action + if not name: + name = basename(path) + self.__add_remote_staging_input(action, name, type) + get_path = lambda: job_directory.calculate_path(name, type) + register = self.rewrite_paths or type == 'tool' # Even if inputs not rewritten, tool must be. + if register: + self.register_rewrite(path, get_path(), type, force=True) + # else: # No action for this file + + def __add_remote_staging_input(self, action, name, type): + input_dict = dict( + name=name, + type=type, + action=action.to_dict(), + ) + self.remote_staging_actions.append(input_dict) + + def __action_for_transfer(self, path, type, contents): if contents: # If contents loaded in memory, no need to write out file and copy, # just transfer. - action_type = 'transfer' + action = MessageAction(contents=contents, client=self.client) else: if not exists(path): message = "handle_tranfer called on non-existent file - [%s]" % path log.warn(message) raise Exception(message) - action_type = self.__action(path, type).action_type - - if action_type in ['transfer', 'copy']: - response = self.client.put_file(path, type, name=name, contents=contents) - register = self.rewrite_paths or type == 'tool' # Even if inputs not rewritten, tool must be. - if register: - self.register_rewrite(path, response['path'], type, force=True) - elif action_type == 'none': - # No action for this file. - pass - else: - raise Exception("Unknown action type (%s) encountered for path (%s)" % (action_type, path)) + action = self.__action(path, type) + return action def register_rewrite(self, local_path, remote_path, type, force=False): action = self.__action(local_path, type) diff -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 -r 423a2939e224a294ded5842daa485da0a007fcbb lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -46,6 +46,13 @@ return contents +def filter_destination_params(destination_params, prefix): + destination_params = destination_params or {} + return dict([(key[len(prefix):], destination_params[key]) + for key in destination_params + if key.startswith(prefix)]) + + class PathHelper(object): ''' 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.

1 0

commit/galaxy-central: martenson: admin/users: show time created and activated status columns to help admins to manage users
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11744e84d4d2/ Changeset: 11744e84d4d2 User: martenson Date: 2014-02-17 19:58:55 Summary: admin/users: show time created and activated status columns to help admins to manage users Affected #: 1 file diff -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a -r 11744e84d4d2389a28ff8e1929d3b4f5eafb21f0 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -56,6 +56,15 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class TimeCreatedColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + return user.create_time.strftime('%x') + class ActivatedColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.active: + return 'Y' + else: + return 'N' # Grid definition title = "Users" @@ -79,6 +88,8 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + TimeCreatedColumn( "Created", attach_popup=False ), + ActivatedColumn( "Activated", attach_popup=False ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] 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.

1 0

commit/galaxy-central: inithello: Remove tool that was migrated to the tool shed in 10719:c2f06b5cfba1. Remove test data that belonged to tools that were removed in 12288:401ee23dcf2f.
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f68bd3660813/ Changeset: f68bd3660813 User: inithello Date: 2014-02-17 19:05:00 Summary: Remove tool that was migrated to the tool shed in 10719:c2f06b5cfba1. Remove test data that belonged to tools that were removed in 12288:401ee23dcf2f. Affected #: 34 files diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/branchlength_in.fasta --- a/test-data/branchlength_in.fasta +++ /dev/null @@ -1,44 +0,0 @@ ->hg17.chr7(+):26907301-26907310|hg17_0 -GTGGGAGGT ->panTro1.chr6(+):28037319-28037328|panTro1_0 -GTGGGAGGT ->mm5.chr6(+):52104022-52104031|mm5_0 -GTGGGAGGT ->rn3.chr4(+):80734395-80734404|rn3_0 -GTGGGAGGT ->canFam1.chr14(+):42826409-42826418|canFam1_0 -GTGGGAGGT - ->hg17.chr7(+):26907310-26907326|hg17_1 -AGTCAGAGTGTCTGAG ->panTro1.chr6(+):28037328-28037344|panTro1_1 -AGTCAGAGTGTCTGAG ->mm5.chr6(+):52104031-52104047|mm5_1 -AGTCAGAGTGTCTGAG ->rn3.chr4(+):80734404-80734420|rn3_1 -AGTCAGAGTATCTGAG ->canFam1.chr14(+):42826418-42826434|canFam1_1 -AGTCAGAGTGTCTGAG - ->hg17.chr7(+):26907326-26907338|hg17_2 -GTAGAAGACCCC ->panTro1.chr6(+):28037344-28037356|panTro1_2 -GTAGAAGACCCC ->mm5.chr6(+):52104047-52104059|mm5_2 -GTAGACGATGCC ->rn3.chr4(+):80734420-80734432|rn3_2 -GTAGATGATGCG ->canFam1.chr14(+):42826434-42826446|canFam1_2 -GTAGAAGACCCC - ->hg17.chr7(+):26907338-26907654|hg17_3 -GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC ->panTro1.chr6(+):28037356-28037672|panTro1_3 -GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC ->mm5.chr6(+):52104059-52104375|mm5_3 -GGAGAAGGGGCACTGGGCGAGGGGCTAGATTTCTCAGATGAT---TCTTCCGTTTTCTCAT-----CGCTGCCAGG----AGGAGTGGCAGGGGAGATGGGCAGGAGCCCCTCCTTCTCACGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGCTGTAGGGACGCGGCAATCTCCACCCTGCGCGCTCGTGTAAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAATTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC ->rn3.chr4(+):80734432-80734748|rn3_3 -GGAGAAGGGGCGCTGGGCGAGGAGCTGGATTTCTCAGATGAT---TCTTCAGTTTTCTCAT-----CGCTTCCAGG----AGGGGTGGCGGGTGAAATGGGCAAGAGCCCCTCTTTCTCGCGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGTTGCAGGGACGCGGCTATCTCCACCCTGCGGGCTCTTGTTAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAGTTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCATACTCTCCAACTTTCC ->canFam1.chr14(+):42826446-42826762|canFam1_3 -GGAGACGGAATGCAGGGCGAGGAGCTGGATTTCTCTGAAGAT---TCCTCCGCCTTCTCCT-----CACTTCCTGG----CGGGGTGGCAGGGGAGATGGGCAAAAGGCCCTCTTTCTCTCGTTTCTTCTGCTTCATCCGGCGGTTCTGGAACCAGATCTTCACCTGGGTCTCGTTGAGCTGCAGGGATGCTGCGATCTCCACCCTGCGGGCGCGGGTCAGATACTTATTGAAGTGGAACTCCTTTTCCAGCTCGGTGAGCTGCTTGGTGGTGAAGTTGGTACGCACTGCATTCGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC - diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/branchlength_out.tabular --- a/test-data/branchlength_out.tabular +++ /dev/null @@ -1,33 +0,0 @@ -Block Branch Length LowerBound UpperBound -1 hg17.chr7(+):26907301-26907310|hg17_0 0 0 0.235398 -1 panTro1.chr6(+):28037319-28037328|panTro1_0 0 0 0.235398 -1 Node1 0 0 0.235398 -1 mm5.chr6(+):52104022-52104031|mm5_0 0 0 0.235398 -1 rn3.chr4(+):80734395-80734404|rn3_0 0 0 0.235398 -1 Node4 0 0 0.235398 -1 canFam1.chr14(+):42826409-42826418|canFam1_0 0 0 0.235398 -1 Total Tree 0 0 0 -2 hg17.chr7(+):26907310-26907326|hg17_1 0 0 0.13592 -2 panTro1.chr6(+):28037328-28037344|panTro1_1 0 0 0.13592 -2 Node1 0 0 0.13592 -2 mm5.chr6(+):52104031-52104047|mm5_1 0 0 0.13592 -2 rn3.chr4(+):80734404-80734420|rn3_1 0.069102 0.00372954 0.421886 -2 Node4 0 0 0.13592 -2 canFam1.chr14(+):42826418-42826434|canFam1_1 0 0 0.13592 -2 Total Tree 0.069102 0.00372954 0.421893 -3 hg17.chr7(+):26907326-26907338|hg17_2 0 0 0.167602 -3 panTro1.chr6(+):28037344-28037356|panTro1_2 0 0 0.167602 -3 Node1 0 0 0.167602 -3 mm5.chr6(+):52104047-52104059|mm5_2 0 0 0.250304 -3 rn3.chr4(+):80734420-80734432|rn3_2 0.198834 0.0311152 0.746578 -3 Node4 0.3077 0.0691968 1.10319 -3 canFam1.chr14(+):42826434-42826446|canFam1_2 0 0 0.167602 -3 Total Tree 0.506533 0.169204 1.27895 -4 hg17.chr7(+):26907338-26907654|hg17_3 0 0 0.0061265 -4 panTro1.chr6(+):28037356-28037672|panTro1_3 0 0 0.0061265 -4 Node1 0.058307 0.0318704 0.0951274 -4 mm5.chr6(+):52104059-52104375|mm5_3 0.0357629 0.0167852 0.0644078 -4 rn3.chr4(+):80734432-80734748|rn3_3 0.0320295 0.0141343 0.0594854 -4 Node4 0.0770194 0.0463495 0.118484 -4 canFam1.chr14(+):42826446-42826762|canFam1_3 0.0575357 0.0316289 0.0936537 -4 Total Tree 0.260654 0.205256 0.325686 diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in1.pileup --- a/test-data/column_join_in1.pileup +++ /dev/null @@ -1,30 +0,0 @@ -chrM 1 A G 25 0 25 1 ^:. I -chrM 2 C T 25 0 25 2 .N I$ -chrM 3 T G 27 0 25 2 .. II -chrM 4 G C 36 0 25 3 .^:.^:. II+ -chrM 5 T A 38 0 25 3 ... III -chrM 6 T A 39 0 25 4 .N.. I$II -chrM 7 G C 43 0 25 5 ...^:.^:. IIIII -chrM 8 A C 46 0 25 6 .....^:. IIIIII -chrM 9 T G 53 0 25 8 ..G...^:.^:. IIIII$II -chrM 10 T G 56 0 25 9 ........^:. IIIIIIIII -chrM 11 C G 57 0 25 10 .........^:. IIIIIIIIII -chrM 12 T C 61 0 25 11 ..........^:. IIIIIIIIIII -chrM 13 T G 79 0 25 15 .........^:.^:.^:.^:.^:.^:. IIIIIIIIIIII#II -chrM 14 A C 58 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII -chrM 15 G A 87 0 25 19 ..N...............^:.^:. DIIIIII$(IIIIIIIIIII -chrM 16 G C 88 0 25 20 .........N.......... IIIIIIIIIIIIIIIIIIII -chrM 17 A C 88 0 25 20 .........G.......... 9IIIIIIIIIIIIIIIIIII -chrM 18 G A 89 0 25 20 ...A................ @IIIIIIIIIIIIIIIIIII -chrM 19 G T 58 0 25 20 ....T.............GG IIIIIIIIIIIIIIIIII'A -chrM 20 T C 55 0 25 20 .........C........C. IIIIIIIIIIIIIII2II#$ -chrM 21 C T 87 0 25 20 ..........G......... IIIIIIIIIIIIIIIIIIII -chrM 22 C A 87 0 25 20 ..........N......... IIIIIIIIIIIIIIAIIIII -chrM 23 A G 87 0 25 20 .....T.............. 9IIIIIIIIII0IIIIIIII -chrM 24 A T 89 0 25 20 .....N..N........... III$IIII"IIIIICII#II -chrM 25 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII -chrM 26 C G 58 0 25 22 ...N....A............. IIHIDII&IIIIII@IIIIII -chrM 27 T A 99 0 25 23 ....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIII -chrM 28 A C 99 0 25 24 ..G..................... 1FIIIIIIIIIIIIIIIIDEIIII -chrM 29 G C 58 0 25 25 ........C.........NN.... ;IIIIII+HII=III$III""IIII -chrM 30 T T 65 0 25 25 ...C....................^:. ;I?&IAI0IIIIIIIIIIIIIIIII diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in10.pileup --- a/test-data/column_join_in10.pileup +++ /dev/null @@ -1,26 +0,0 @@ -0610009D07Rik 2 1.41 1.41 -0.24 12/12 2 1 -1110002N22Rik 2 1.70 1.70 -0.06 10/12 2 1 -1110008L16Rik 3 1.73 1.73 -0.54 12/12 2 1 -1110054O05Rik 1 1.55 1.55 1.14 5/12 1 1 -Actg1 2 4.24 4.24 2.36 4/12 2 1 -Actl6a 2 1.55 1.55 1.00 10/12 1 1 -Actn1 1 3.46 3.46 3.17 1/12 1 1 -Actn4 1 3.46 3.46 3.17 1/12 1 1 -Bnc2 1 2.00 2.00 1.67 3/12 1 1 -Bub3 2 1.89 1.89 1.02 9/12 2 1 -Cad 4 4.90 4.90 3.09 2/12 1 1 -Calm1;Calm3;Calm2 2 2.83 2.83 2.57 3/12 1 1 -E130012A19Rik 2 5.66 5.66 1.50 3/12 2 1 -E2f6 2 3.39 3.39 1.80 5/12 2 1 -Gm12620 1 3.46 3.46 3.17 1/12 1 1 -Gm13092;LOC677017 1 1.15 1.15 0.29 9/12 1 1 -Gm14173;Rpl37a;Gm4149 1 3.00 3.00 1.37 4/12 2 1 -Gm14393;2210418O10Rik;Gm14296;Gm14401;RP23-330D3.5 1 3.46 3.46 3.17 1/12 1 1 -Gm189 1 1.20 1.20 0.16 10/12 2 1 -Sfrs7 1 1.71 1.71 0.18 7/12 2 1 -Sin3a 1 1.71 1.71 -0.12 7/12 2 1 -Ski 1 2.45 2.45 2.13 2/12 1 1 -Skil 1 2.00 2.00 1.03 3/12 1 1 -Tubb2c 1 2.00 2.00 1.67 3/12 1 1 -Tubb2c-ps1 1 12.00 12.00 3.17 1/12 2 1 -Zscan4f 2 1.70 1.70 1.00 10/12 2 1 diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in11.pileup --- a/test-data/column_join_in11.pileup +++ /dev/null @@ -1,36 +0,0 @@ -0610009D07Rik 3 1.73 1.73 1.15 12/12 2 1 -0610010K14Rik 1 1.41 1.41 0.96 6/12 1 1 -1110002N22Rik 3 2.08 2.08 0.74 10/12 2 1 -1110008L16Rik 1 1.00 1.00 -1.35 12/12 1 1 -Acta1 2 1.54 1.54 0.63 11/12 2 1 -Actb 1 1.33 1.33 0.00 9/12 2 1 -Actg1 1 3.00 3.00 0.87 4/12 2 1 -Actl6a 1 1.10 1.10 -0.33 10/12 1 1 -Actl6b 1 2.45 2.45 2.13 2/12 1 1 -Bnc2 1 2.00 2.00 1.67 3/12 1 1 -Bptf 1 3.46 3.46 3.17 1/12 1 1 -Brip1 1 1.22 1.22 -0.19 8/12 1 1 -Brms1l 1 12.00 12.00 3.17 1/12 2 1 -Btf3;Gm3531 1 2.00 2.00 1.67 3/12 1 1 -Bub3 3 2.00 2.00 2.13 9/12 1 1 -C330007P06Rik 1 2.45 2.45 2.13 2/12 1 1 -Cad 1 2.45 2.45 0.50 2/12 1 1 -Calm1;Calm3;Calm2 1 2.00 2.00 1.03 3/12 1 1 -Cbx1 2 3.39 3.39 2.24 5/12 2 1 -E2f6 1 2.40 2.40 0.53 5/12 2 1 -Eed 1 1.20 1.20 -0.47 10/12 2 1 -Gm10079 2 1.41 1.41 0.16 12/12 1 1 -Gm11230 2 1.48 1.48 1.21 11/12 1 1 -Gm13072;Trmt112 1 3.46 3.46 3.17 1/12 1 1 -Gm13092;LOC677017 1 1.33 1.33 0.29 9/12 2 1 -Gm14231 1 1.31 1.31 0.51 7/12 1 1 -Gm14456;Tpt1 1 2.00 2.00 1.67 3/12 1 1 -Gm15501;Rps8 1 1.55 1.55 1.14 5/12 1 1 -Gm189 1 1.20 1.20 0.16 10/12 2 1 -Sfrs11 3 1.73 1.73 1.15 12/12 2 1 -Sin3a 4 3.43 3.43 1.93 7/12 2 1 -Sirt7 1 2.00 2.00 1.67 3/12 1 1 -Skiv2l2 12 3.46 3.46 -0.72 12/12 2 1 -Tubb2b 4 2.00 2.00 0.49 12/12 2 1 -Zscan4e 1 1.41 1.41 0.63 6/12 1 1 -Zscan4f 2 1.70 1.70 1.00 10/12 2 1 diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in12.pileup --- a/test-data/column_join_in12.pileup +++ /dev/null @@ -1,36 +0,0 @@ -0610009D07Rik 4 2.00 2.00 2.54 12/12 2 1 -0610010K14Rik 1 1.41 1.41 0.96 6/12 1 1 -1110002N22Rik 2 1.70 1.70 -0.06 10/12 2 1 -1110008L16Rik 6 2.45 2.45 0.68 12/12 2 1 -1110037F02Rik 1 2.45 2.45 2.13 2/12 1 1 -1190005F20Rik 4 2.18 2.18 0.28 11/12 2 1 -Acot8 1 2.00 2.00 0.07 6/12 2 1 -Acta1 2 1.54 1.54 0.63 11/12 2 1 -Actb 2 1.89 1.89 1.35 9/12 2 1 -Actl6b 1 6.00 6.00 2.13 2/12 2 1 -Bend3 1 1.15 1.33 -0.51 9/12 1 1.33 -Bend5 1 3.46 3.46 3.17 1/12 1 1 -Brip1 2 1.73 1.73 0.58 8/12 1 1 -Btf3;Gm3531 1 4.00 4.00 1.67 3/12 2 1 -Bub3 1 1.33 1.33 -0.09 9/12 2 1 -C130039O16Rik 1 2.45 2.45 2.13 2/12 1 1 -C1d 1 1.73 1.73 0.87 4/12 1 1 -Caprin1 2 2.42 2.42 0.51 7/12 2 1 -Cbx3 2 1.54 1.54 0.75 11/12 2 1 -Eed 1 1.10 1.10 -0.47 10/12 1 1 -Efha1 1 3.46 3.46 3.17 1/12 1 1 -Exosc1 3 1.73 1.73 1.29 12/12 2 1 -Exosc10 25 5.00 5.00 1.03 12/12 2 1 -Gm189 2 1.70 1.70 2.12 10/12 2 1 -Gm3200 1 2.45 2.45 2.13 2/12 1 1 -Gm9855;Tdg 2 1.70 1.70 1.37 10/12 2 1 -Sfrs11 4 2.00 2.00 2.54 12/12 2 1 -Sfrs12 2 5.66 5.66 2.57 3/12 2 1 -Sin3a 1 1.31 1.31 -0.12 7/12 1 1 -Sirt7 1 2.00 2.00 1.67 3/12 1 1 -Skiv2l2 34 5.83 5.83 0.68 12/12 2 1 -Tubb2b 3 1.73 1.73 -0.10 12/12 2 1 -Tubb4 1 1.15 1.15 0.29 9/12 1 1 -Zscan4-ps2 1 12.00 12.00 3.17 1/12 2 1 -Zscan4e 2 2.83 2.83 2.12 6/12 2 1 -Zscan4f 2 1.70 1.70 1.00 10/12 2 1 diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in13.tabular --- a/test-data/column_join_in13.tabular +++ /dev/null @@ -1,6 +0,0 @@ -alpha beta gamma delta -1 A I a i -2 B II b ii -5 C III c -7 D IV d iii -11 E V e iv diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in14.tabular --- a/test-data/column_join_in14.tabular +++ /dev/null @@ -1,11 +0,0 @@ -alpha beta gamma delta epsilon -1 AA I2 aa i2 -2 BB II2 bb -3 CC III2 cc ii2 -4 DD IV2 dd iii2 -6 EE V2 ee iv2 -7 FF VI2 ff -8 GG VII2 gg v2 -9 HH VIII2 hh vi2 -10 II IX2 ii vii2 -11 JJ X2 jj viii2 diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in15.tabular --- a/test-data/column_join_in15.tabular +++ /dev/null @@ -1,11 +0,0 @@ -alpha beta gamma -2 BBB II3 bbb i3 -3 CCC III3 ccc ii3 -4 DDD IV2 ddd iii3 -5 EEE V3 eee -6 FFF VI3 fff iv3 -7 GGG VII3 ggg v3 -8 HHH VIII3 hhh -9 III IX3 iii vi3 -10 JJJ X3 jjj vii3 -11 LLL XI3 lll diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in2.pileup --- a/test-data/column_join_in2.pileup +++ /dev/null @@ -1,30 +0,0 @@ -chrM 1 T G 25 0 25 1 ^:. I -chrM 2 C A 25 0 25 1 . I -chrM 3 C A 25 0 25 2 .. I+ -chrM 4 G A 36 0 25 3 .^:.^:. II+ -chrM 5 A T 36 0 25 3 ... IDI -chrM 6 A G 36 0 25 4 ..T. IIBI -chrM 7 C G 42 0 25 5 ...^:.^:. ID@II -chrM 8 T T 45 0 25 6 .....^:. III$BI -chrM 9 C A 51 0 25 8 ......^:.^:. $#III+III -chrM 10 G G 54 0 25 9 ........^:. III$III#I -chrM 11 T C 57 0 25 10 .........^:. IIIDBIIIII -chrM 12 A T 60 0 25 11 ..........^:. IIIIIIIII$I -chrM 13 A T 78 0 25 18 ..A.........^:.^:.^:.^:.^:.^:. III#$IIIIII+IIDIIB -chrM 14 G A 56 0 25 19 ........T.........^:. BIIIIIII+IIII$IBIII -chrM 15 G A 87 0 25 20 ..................^:.^:. DIIIIIII(IIIIIIIIIII -chr1 1 T T 87 0 25 20 .............T...... IIIIIIIIIIII$DIIIIII -chr1 2 A T 87 0 25 20 ......G............. 9IIIIIIIIIIIIICBIIII -chr1 3 A G 87 0 25 20 ....A............... @IIIIIIIII#IIII#IIII -chr1 4 A T 55 0 25 20 ..................GG IIIII@II$IIIIIIIII'A -chr1 5 C A 54 0 25 20 .......A..........C. IIIIIIIIIDIIIII2II#$ -chr1 6 G T 87 0 25 20 .............A...... IIIIIIIBIIIIII#IIIII -chr1 7 A C 87 0 25 20 ..........C......... IIIII+IIIIIIIIAIIIII -chr1 8 G A 87 0 25 20 ....G.........T..... 9IIIIIIIIII0IIIIIIII -chr1 9 A T 87 0 25 20 ........N........... IIII$III"IIIIICIIIII -chr1 10 G A 57 0 25 21 ...A................^:. A@.$IIIIIIIFIIIIIIIII -chr1 11 C A 57 0 25 22 ....G...A............. IIHIDII&IIIIII#III$II -chr1 12 T A 99 0 25 24 .....................^:.^:.^:. IE8IFIII9IIIIIIIIIIIIIII -chr1 13 A C 99 0 25 25 ...N..................... 1FIIIIIIIIIIIIIIIIDEII$II -chr1 14 G C 55 0 25 25 ....G..............NN.... ;IIIBIII+HII=IIIIII""IIII -chr1 15 T G 68 0 25 28 ...C.......N............^:. ;I?&IAI0IIIIIII@II#$II@II diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in3.pileup --- a/test-data/column_join_in3.pileup +++ /dev/null @@ -1,30 +0,0 @@ -chr1 1 G G 25 0 25 1 ^:. I -chr1 2 T T 25 0 25 1 . I -chr1 3 T T 27 0 25 1 . I -chr1 4 A A 36 0 25 2 .^:. I+ -chr1 5 A A 36 0 25 3 ... III -chr1 6 T T 36 0 25 4 .N.. II#I -chr1 7 G G 42 0 25 5 ...^:.^:. IIIII -chr1 8 T T 45 0 25 6 .....^:. IIIIII -chr1 9 A A 51 0 25 7 .....^:.^:. IBIIIII -chr1 10 G G 54 0 25 9 ........^:. IIIIIIIII -chr1 11 C C 57 0 25 10 .........^:. IIIIIIII"I -chr1 12 T T 60 0 25 11 ..........^:. IIIIIIDIIII -chr1 13 T T 78 0 25 17 ...........^:.^:.^:.^:.^:.^:. IIII"$IIIIIIIIIII -chr1 14 A A 56 0 25 18 .......G.........^:. BIIIIIII+IIIIIIIII -chr1 15 A A 87 0 25 20 ....N.............^:.^:. DIII$III(IIIIIIIIIII -chr4 1 T T 90 0 25 20 ..........N......... IIIIIIIII$IIIIIIIIII -chr4 2 A A 87 0 25 20 .......C............ 9IIIIIIIII"IIIIIIIII -chr4 3 A A 34 0 25 20 ......G............. @IIIIIIIIIIII#IIIIII -chr4 4 T T 55 0 25 21 ...........N.......GG IIIII@IIIIIIIIIIIII'A -chr4 5 A A 54 0 25 21 ...N...............C. IIII"IIIIIIIIIII2II#$ -chr4 6 T T 87 0 25 21 ................N.... IIIIIIII$IIIIIIIIIIII -chr4 7 A A 80 0 25 21 .....G............... III$IIIIIIIIIIIAIIIII -chr4 8 A A 87 0 25 22 ..N................... 9IIIIIIIIII0IIIII"$III -chr4 9 A A 87 0 25 22 .GG.......N........... IIII$IIIII"IIIIICIIIII -chr4 10 G G 57 0 25 23 .....A................^:. A@.$IIIIIIIIIFIIIIIIIII -chr4 11 C C 57 0 25 25 .......A.....GN.......... IIHIDII&III#IIIIIIIIIIIII -chr4 12 A A 99 0 25 26 .......................^:.^:.^:. IE8IFIII9IIIIIII$IIIIIIIII -chr4 13 A A 99 0 25 27 ........N.................. 1FIIIIII$IIIIIIIIIIIIDEIIII -chr4 14 G G 55 0 25 28 ..N...................NN.... ;III$I#IIII+HII=IIIIII""IIII -chr4 15 G G 68 0 25 30 ...C....N..G.................^:. ;I?&IAI0IIIIIII$#I$@IIIIIIIIII diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in4.pileup --- a/test-data/column_join_in4.pileup +++ /dev/null @@ -1,25 +0,0 @@ -chr2 1 T 6 .C..., I$$III -chr2 2 G 6 ..N.., III@II -chr2 3 C 7 ..C..., I$IIIII -chr2 4 G 7 .G...., I#IIIII -chr2 5 G 7 ...N.., IIII#BI -chr2 6 A 7 ..T..., I$IDIII -chr2 7 T 8 ...C..., IIIBD$II -chr2 8 A 8 ..A...., IBI#IIII -chr2 9 C 9 .GA..N.., I$IBIII#I -chr2 10 T 9 ........, I$II#IIII -chr2 11 C 10 .>>..T..., IIII@I$I$I -chr2 12 G 10 .N..G...., III$IIIIII -chr2 13 A 11 ....A..T.., IIIIII#I@II -chr1 1 C 1 ^:. I -chr1 2 G 2 .^:. $I -chr1 3 A 2 .. I% -chr1 4 C 2 .. I$ -chr1 5 T 3 ..^:. I#I -chr1 6 G 3 ..^:, I#I -chr1 7 C 4 .N., IIII -chr1 8 A 4 ..., I$II -chr1 9 T 5 ..C., I#IDI -chr1 10 G 5 N..., IBII@ -chr1 11 A 5 .C.., I$II# -chr1 12 C 5 ..N., I$III diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in5.pileup --- a/test-data/column_join_in5.pileup +++ /dev/null @@ -1,25 +0,0 @@ -chr1 42 T 1 ^:. I -chr1 43 G 2 .^:. $I -chr1 44 T 2 .. I% -chr1 45 C 3 ..^:. III -chr1 46 G 3 ..^:. I#I -chr1 47 T 4 ...^:, I#II -chr1 48 A 4 .N., IIII -chr1 49 C 5 ...., IIIII -chr1 50 A 5 ..G., IIIDI -chr1 51 A 5 A..., IBIII -chr1 52 A 5 ...., IIII# -chr1 53 G 5 ..N., I$III -chr2 77 C 6 .G..., I$$III -chr2 78 G 6 ..N.., III@II -chr2 79 T 7 ..N..., I$IIIII -chr2 80 C 7 .G...., I#IIIII -chr2 81 G 7 ...A.., IIII#BI -chr2 82 A 8 ...G..., I$IDIIII -chr2 83 A 8 ...T..., IIIBD$II -chr2 84 T 8 ..A...., IBI#IIII -chr2 85 G 8 .GA...., IIBIII#I -chr2 86 C 9 ........, I$II#IIII -chr2 87 G 9 ....T..., IIIII$I$I -chr2 88 G 10 .N..G...., III$IIIIII -chr2 89 G 10 ...A..T.., IIIII#I@II diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in6.pileup --- a/test-data/column_join_in6.pileup +++ /dev/null @@ -1,25 +0,0 @@ -chr1 42 C 1 ^:. I -chr1 43 C 2 .^:. II -chr1 44 T 2 .. II -chr1 45 A 3 ..^:. III -chr1 46 G 4 ...^:. IIII -chr1 47 A 5 ....^:, IIIII -chr1 48 T 5 ...N, I#III -chr1 49 G 5 ...., IIIII -chr1 50 A 5 .G.., IIIII -chr1 51 G 5 ...., IIIII -chr2 52 T 5 .N.., II$II -chr2 53 A 5 ...., IIIII -chr2 54 T 5 ...., IIIII -chr2 55 T 5 ...., IIIII -chr2 56 C 5 ...., IIIBI -chr2 57 T 5 ...., IDIII -chr2 58 T 6 .N..., IIIIII -chr2 59 A 6 ....., IIII$I -chr3 60 C 6 ...G., I#IIII -chr3 61 T 6 ..N.., IIIIII -chr3 62 C 6 ...A., IIIIII -chr3 63 C 7 .N...., IIIIIII -chr3 64 A 7 ...G.., IIIII$I -chr3 65 T 7 ...AA., IIIII@@ -chr3 66 A 7 ....N., IIIIIII diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in7.pileup --- a/test-data/column_join_in7.pileup +++ /dev/null @@ -1,32 +0,0 @@ -chr2 1 T 6 .C..., I$$III -chr2 2 G 6 ..N.., III@II -chr2 3 C 7 ..C..., I$IIIII -chr2 4 G 7 .G...., I#IIIII -chr2 5 G 7 ...N.., IIII#BI -chr2 6 A 7 ..T..., I$IDIII -chr2 7 T 8 ...C..., IIIBD$II -chr2 8 A 8 ..A...., IBI#IIII -chr2 9 C 9 .GA..N.., I$IBIII#I -chr2 10 T 9 ........, I$II#IIII -chr2 11 C 10 .>>..T..., IIII@I$I$I -chr2 12 G 10 .N..G...., III$IIIIII -chr2 13 A 11 ....A..T.., IIIIII#I@II -chr2 14 G 11 ..N....... IICIBII@AII -chr2 15 C 11 A.....NG.. IIIIIDIIIII -chr2 16 T 11 ...C.....G I$IIIB@IIIC -chr2 17 C 12 G......TN.. IIAII@IIII$I -chr2 18 A 12 N......G..A IIIBIII$IIII -chr2 19 A 13 .......NN... IIIIIIBIII$$@ -chr2 20 C 13 ..GT.......N IIIIABIIC$III -chr1 1 C 1 ^:. I -chr1 2 G 2 .^:. $I -chr1 3 A 2 .. I% -chr1 4 C 2 .. I$ -chr1 5 T 3 ..^:. I#I -chr1 6 G 3 ..^:, I#I -chr1 7 C 4 .N., IIII -chr1 8 A 4 ..., I$II -chr1 9 T 5 ..C., I#IDI -chr1 10 G 5 N..., IBII@ -chr1 11 A 5 .C.., I$II# -chr1 12 C 5 ..N., I$III diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in8.pileup --- a/test-data/column_join_in8.pileup +++ /dev/null @@ -1,23 +0,0 @@ -chr1 42 T 1 ^:. I -chr1 43 G 2 .^:. $I -chr1 44 T 2 .. I% -chr1 45 C 3 ..^:. III -chr1 46 G 3 ..^:. I#I -chr1 47 T 4 ...^:, I#II -chr1 48 A 4 .N., IIII -chr1 49 C 5 ...., IIIII -chr1 50 A 5 ..G., IIIDI -chr1 51 A 5 A..., IBIII -chr1 52 A 5 ...., IIII# -chr1 53 G 5 ..N., I$III -chr2 77 C 6 .G..., I$$III -chr2 78 G 6 ..N.., III@II -chr2 79 T 7 ..N..., I$IIIII -chr2 80 C 7 .G...., I#IIIII -chr2 81 G 7 ...A.., IIII#BI -chr2 82 A 8 ...G..., I$IDIIII -chr2 83 A 8 ...T..., IIIBD$II -chr2 84 T 8 ..A...., IBI#IIII -chr2 85 G 8 .GA...., IIBIII#I -chr2 86 C 9 ........, I$II#IIII -chr2 87 G 9 ....T..., IIIII$I$I diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_in9.pileup --- a/test-data/column_join_in9.pileup +++ /dev/null @@ -1,25 +0,0 @@ -chr1 43 C 2 .^:. II -chr3 65 T 7 ...AA., IIIII@@ -chr1 44 T 2 .. II -chr2 54 T 5 ...., IIIII -chr1 45 A 3 ..^:. III -chr1 47 A 5 ....^:, IIIII -chr1 50 A 5 .G.., IIIII -chr1 51 G 5 ...., IIIII -chr2 52 T 5 .N.., II$II -chr2 53 A 5 ...., IIIII -chr3 60 C 6 ...G., I#IIII -chr3 61 T 6 ..N.., IIIIII -chr1 49 G 5 ...., IIIII -chr2 55 T 5 ...., IIIII -chr2 56 C 5 ...., IIIBI -chr2 58 T 6 .N..., IIIIII -chr2 59 A 6 ....., IIII$I -chr3 62 C 6 ...A., IIIIII -chr1 42 C 1 ^:. I -chr3 63 C 7 .N...., IIIIIII -chr1 48 T 5 ...N, I#III -chr1 46 G 4 ...^:. IIII -chr3 64 A 7 ...G.., IIIII$I -chr3 66 A 7 ....N., IIIIIII -chr2 57 T 5 ...., IDIII diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_out1.pileup --- a/test-data/column_join_out1.pileup +++ /dev/null @@ -1,60 +0,0 @@ -chr1 1 ? ? ? ? T T 87 25 G G 25 25 -chr1 2 ? ? ? ? A T 87 25 T T 25 25 -chr1 3 ? ? ? ? A G 87 25 T T 27 25 -chr1 4 ? ? ? ? A T 55 25 A A 36 25 -chr1 5 ? ? ? ? C A 54 25 A A 36 25 -chr1 6 ? ? ? ? G T 87 25 T T 36 25 -chr1 7 ? ? ? ? A C 87 25 G G 42 25 -chr1 8 ? ? ? ? G A 87 25 T T 45 25 -chr1 9 ? ? ? ? A T 87 25 A A 51 25 -chr1 10 ? ? ? ? G A 57 25 G G 54 25 -chr1 11 ? ? ? ? C A 57 25 C C 57 25 -chr1 12 ? ? ? ? T A 99 25 T T 60 25 -chr1 13 ? ? ? ? A C 99 25 T T 78 25 -chr1 14 ? ? ? ? G C 55 25 A A 56 25 -chr1 15 ? ? ? ? T G 68 25 A A 87 25 -chr4 1 ? ? ? ? ? ? ? ? T T 90 25 -chr4 2 ? ? ? ? ? ? ? ? A A 87 25 -chr4 3 ? ? ? ? ? ? ? ? A A 34 25 -chr4 4 ? ? ? ? ? ? ? ? T T 55 25 -chr4 5 ? ? ? ? ? ? ? ? A A 54 25 -chr4 6 ? ? ? ? ? ? ? ? T T 87 25 -chr4 7 ? ? ? ? ? ? ? ? A A 80 25 -chr4 8 ? ? ? ? ? ? ? ? A A 87 25 -chr4 9 ? ? ? ? ? ? ? ? A A 87 25 -chr4 10 ? ? ? ? ? ? ? ? G G 57 25 -chr4 11 ? ? ? ? ? ? ? ? C C 57 25 -chr4 12 ? ? ? ? ? ? ? ? A A 99 25 -chr4 13 ? ? ? ? ? ? ? ? A A 99 25 -chr4 14 ? ? ? ? ? ? ? ? G G 55 25 -chr4 15 ? ? ? ? ? ? ? ? G G 68 25 -chrM 1 A G 25 25 T G 25 25 ? ? ? ? -chrM 2 C T 25 25 C A 25 25 ? ? ? ? -chrM 3 T G 27 25 C A 25 25 ? ? ? ? -chrM 4 G C 36 25 G A 36 25 ? ? ? ? -chrM 5 T A 38 25 A T 36 25 ? ? ? ? -chrM 6 T A 39 25 A G 36 25 ? ? ? ? -chrM 7 G C 43 25 C G 42 25 ? ? ? ? -chrM 8 A C 46 25 T T 45 25 ? ? ? ? -chrM 9 T G 53 25 C A 51 25 ? ? ? ? -chrM 10 T G 56 25 G G 54 25 ? ? ? ? -chrM 11 C G 57 25 T C 57 25 ? ? ? ? -chrM 12 T C 61 25 A T 60 25 ? ? ? ? -chrM 13 T G 79 25 A T 78 25 ? ? ? ? -chrM 14 A C 58 25 G A 56 25 ? ? ? ? -chrM 15 G A 87 25 G A 87 25 ? ? ? ? -chrM 16 G C 88 25 ? ? ? ? ? ? ? ? -chrM 17 A C 88 25 ? ? ? ? ? ? ? ? -chrM 18 G A 89 25 ? ? ? ? ? ? ? ? -chrM 19 G T 58 25 ? ? ? ? ? ? ? ? -chrM 20 T C 55 25 ? ? ? ? ? ? ? ? -chrM 21 C T 87 25 ? ? ? ? ? ? ? ? -chrM 22 C A 87 25 ? ? ? ? ? ? ? ? -chrM 23 A G 87 25 ? ? ? ? ? ? ? ? -chrM 24 A T 89 25 ? ? ? ? ? ? ? ? -chrM 25 G A 57 25 ? ? ? ? ? ? ? ? -chrM 26 C G 58 25 ? ? ? ? ? ? ? ? -chrM 27 T A 99 25 ? ? ? ? ? ? ? ? -chrM 28 A C 99 25 ? ? ? ? ? ? ? ? -chrM 29 G C 58 25 ? ? ? ? ? ? ? ? -chrM 30 T T 65 25 ? ? ? ? ? ? ? ? diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_out2.pileup --- a/test-data/column_join_out2.pileup +++ /dev/null @@ -1,65 +0,0 @@ -chr1 1 C 1 -chr1 2 G 2 -chr1 3 A 2 -chr1 4 C 2 -chr1 5 T 3 -chr1 6 G 3 -chr1 7 C 4 -chr1 8 A 4 -chr1 9 T 5 -chr1 10 G 5 -chr1 11 A 5 -chr1 12 C 5 -chr1 42 T 1 C 1 -chr1 43 G 2 C 2 -chr1 44 T 2 T 2 -chr1 45 C 3 A 3 -chr1 46 G 3 G 4 -chr1 47 T 4 A 5 -chr1 48 A 4 T 5 -chr1 49 C 5 G 5 -chr1 50 A 5 A 5 -chr1 51 A 5 G 5 -chr1 52 A 5 -chr1 53 G 5 -chr2 1 T 6 -chr2 2 G 6 -chr2 3 C 7 -chr2 4 G 7 -chr2 5 G 7 -chr2 6 A 7 -chr2 7 T 8 -chr2 8 A 8 -chr2 9 C 9 -chr2 10 T 9 -chr2 11 C 10 -chr2 12 G 10 -chr2 13 A 11 -chr2 52 T 5 -chr2 53 A 5 -chr2 54 T 5 -chr2 55 T 5 -chr2 56 C 5 -chr2 57 T 5 -chr2 58 T 6 -chr2 59 A 6 -chr2 77 C 6 -chr2 78 G 6 -chr2 79 T 7 -chr2 80 C 7 -chr2 81 G 7 -chr2 82 A 8 -chr2 83 A 8 -chr2 84 T 8 -chr2 85 G 8 -chr2 86 C 9 -chr2 87 G 9 -chr2 88 G 10 -chr2 89 G 10 -chr3 60 C 6 -chr3 61 T 6 -chr3 62 C 6 -chr3 63 C 7 -chr3 64 A 7 -chr3 65 T 7 -chr3 66 A 7 diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_out3.pileup --- a/test-data/column_join_out3.pileup +++ /dev/null @@ -1,70 +0,0 @@ -chr1 1 C 1 ^:. X X -chr1 2 G 2 .^:. X X -chr1 3 A 2 .. X X -chr1 4 C 2 .. X X -chr1 5 T 3 ..^:. X X -chr1 6 G 3 ..^:, X X -chr1 7 C 4 .N., X X -chr1 8 A 4 ..., X X -chr1 9 T 5 ..C., X X -chr1 10 G 5 N..., X X -chr1 11 A 5 .C.., X X -chr1 12 C 5 ..N., X X -chr1 42 X T 1 ^:. C 1 ^:. -chr1 43 X G 2 .^:. C 2 .^:. -chr1 44 X T 2 .. T 2 .. -chr1 45 X C 3 ..^:. A 3 ..^:. -chr1 46 X G 3 ..^:. G 4 ...^:. -chr1 47 X T 4 ...^:, A 5 ....^:, -chr1 48 X A 4 .N., T 5 ...N, -chr1 49 X C 5 ...., G 5 ...., -chr1 50 X A 5 ..G., A 5 .G.., -chr1 51 X A 5 A..., G 5 ...., -chr1 52 X A 5 ...., X -chr1 53 X G 5 ..N., X -chr2 1 T 6 .C..., X X -chr2 2 G 6 ..N.., X X -chr2 3 C 7 ..C..., X X -chr2 4 G 7 .G...., X X -chr2 5 G 7 ...N.., X X -chr2 6 A 7 ..T..., X X -chr2 7 T 8 ...C..., X X -chr2 8 A 8 ..A...., X X -chr2 9 C 9 .GA..N.., X X -chr2 10 T 9 ........, X X -chr2 11 C 10 .>>..T..., X X -chr2 12 G 10 .N..G...., X X -chr2 13 A 11 ....A..T.., X X -chr2 14 G 11 ..N....... X X -chr2 15 C 11 A.....NG.. X X -chr2 16 T 11 ...C.....G X X -chr2 17 C 12 G......TN.. X X -chr2 18 A 12 N......G..A X X -chr2 19 A 13 .......NN... X X -chr2 20 C 13 ..GT.......N X X -chr2 52 X X T 5 .N.., -chr2 53 X X A 5 ...., -chr2 54 X X T 5 ...., -chr2 55 X X T 5 ...., -chr2 56 X X C 5 ...., -chr2 57 X X T 5 ...., -chr2 58 X X T 6 .N..., -chr2 59 X X A 6 ....., -chr2 77 X C 6 .G..., X -chr2 78 X G 6 ..N.., X -chr2 79 X T 7 ..N..., X -chr2 80 X C 7 .G...., X -chr2 81 X G 7 ...A.., X -chr2 82 X A 8 ...G..., X -chr2 83 X A 8 ...T..., X -chr2 84 X T 8 ..A...., X -chr2 85 X G 8 .GA...., X -chr2 86 X C 9 ........, X -chr2 87 X G 9 ....T..., X -chr3 60 X X C 6 ...G., -chr3 61 X X T 6 ..N.., -chr3 62 X X C 6 ...A., -chr3 63 X X C 7 .N...., -chr3 64 X X A 7 ...G.., -chr3 65 X X T 7 ...AA., -chr3 66 X X A 7 ....N., diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_out4.pileup --- a/test-data/column_join_out4.pileup +++ /dev/null @@ -1,65 +0,0 @@ -0610009D07Rik 2 2 3 2 4 2 -0610010K14Rik 1 1 1 1 -1110002N22Rik 2 2 3 2 2 2 -1110008L16Rik 3 2 1 1 6 2 -1110037F02Rik 1 1 -1110054O05Rik 1 1 -1190005F20Rik 4 2 -Acot8 1 2 -Acta1 2 2 2 2 -Actb 1 2 2 2 -Actg1 2 2 1 2 -Actl6a 2 1 1 1 -Actl6b 1 1 1 2 -Actn1 1 1 -Actn4 1 1 -Bend3 1 1 -Bend5 1 1 -Bnc2 1 1 1 1 -Bptf 1 1 -Brip1 1 1 2 1 -Brms1l 1 2 -Btf3;Gm3531 1 1 1 2 -Bub3 2 2 3 1 1 2 -C1d 1 1 -C130039O16Rik 1 1 -C330007P06Rik 1 1 -Cad 4 1 1 1 -Calm1;Calm3;Calm2 2 1 1 1 -Caprin1 2 2 -Cbx1 2 2 -Cbx3 2 2 -E2f6 2 2 1 2 -E130012A19Rik 2 2 -Eed 1 2 1 1 -Efha1 1 1 -Exosc1 3 2 -Exosc10 25 2 -Gm189 1 2 1 2 2 2 -Gm3200 1 1 -Gm9855;Tdg 2 2 -Gm10079 2 1 -Gm11230 2 1 -Gm12620 1 1 -Gm13072;Trmt112 1 1 -Gm13092;LOC677017 1 1 1 2 -Gm14173;Rpl37a;Gm4149 1 2 -Gm14231 1 1 -Gm14393;2210418O10Rik;Gm14296;Gm14401;RP23-330D3.5 1 1 -Gm14456;Tpt1 1 1 -Gm15501;Rps8 1 1 -Sfrs7 1 2 -Sfrs11 3 2 4 2 -Sfrs12 2 2 -Sin3a 1 2 4 2 1 1 -Sirt7 1 1 1 1 -Ski 1 1 -Skil 1 1 -Skiv2l2 12 2 34 2 -Tubb2b 4 2 3 2 -Tubb2c 1 1 -Tubb2c-ps1 1 2 -Tubb4 1 1 -Zscan4-ps2 1 2 -Zscan4e 1 1 2 2 -Zscan4f 2 2 2 2 2 2 diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/column_join_out5.tabular --- a/test-data/column_join_out5.tabular +++ /dev/null @@ -1,12 +0,0 @@ -1 i i2 0 -2 ii 0 i3 -3 0 ii2 ii3 -4 0 iii2 iii3 -5 0 0 0 -6 0 iv2 iv3 -7 iii 0 v3 -8 0 v2 0 -9 0 vi2 vi3 -10 0 vii2 vii3 -11 iv viii2 0 -alpha 0 epsilon 0 diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/dnds_inp.fasta --- a/test-data/dnds_inp.fasta +++ /dev/null @@ -1,76 +0,0 @@ ->human -ATGGCTGTGGCCCTGGGTTGTGCAATCCAGGCATCCTTGAATCAAGGCTCTGTGTTTCAAGAATATGATACTGACTGTGAAGTTTTCCGTCAGCGCTTCAGGCAGTTCCAGTACAGAGAAGCAGCTGGGCCTCATGAAGCATTTAACAAACTCTGGGAGCTTTGCTGTCAATGGCTGAAGCCAAAGATGCGCTCTAAGGAACAAATCCTGGAGCTGCTAGTGTTGGAGCAATTCCTAACTATCCTGCCCACAGAGATAGAGACCTGGGTGAGGGAGCACTGCCCAGAGAATAGAGAAAGAGTTGTGTCACTGATAGAAGACTTACAGAGAGAACTTGAGATACCAGAGCAGCAGGTTGATATGCATGACATGCTCTTGGAAGAACTGGCACCAGTGGGAACGGCACACATACCACCAACCATGCACCTAGAGTCACCTGCACTCCAGGTAATGGGACCTGCCCAGGAGGCCCCAGTAGCAGAGGCATGGATCCCACAGGCAGGGCCACCGGAGCTGAACTATGGTGCTACTGGAGAATGTCAGAACTTTCTGGACCCTGGATATCCATTACCAAAACTTGACATGAACTTCTCATTGGAGAATAGAGAAGAGCCATGGGTGAAGGAATTACAGGATTCTAAAGAAATGAAACAATTACTTGATTCCAAGATAGGTTTTGAGATCGGGATAGAAAATGAAGAAGATACTTCAAAACAGAAAAAAATGGAGACTATGTATCCATTTATTGTAACTTTAGAGGGGAATGCTCTCCAGGGTCCCATTTTGCAAAAAGACTATGTACAGTTAGAAAATCAATGGGAAACCCCCCCAGAGGATTTACAGACAGATTTAGCAAAACTGGTAGATCAGCAGAACCCCACTCTGGGAGAGACACCTGAGAACTCCAACTTGGAAGAACCTCTCAACCCTAAACCCCACAAGAAAAAGAGTCCAGGAGAGAAACCTCACCGATGTCCTCAGTGTGGAAAATGTTTTGCTCGGAAGTCACAACTTACTGGGCATCAGAGAATTCATTCAGGAGAAGAACCTCACAAATGCCCTGAATGTGGGAAAAGATTCCTTCGTAGTTCAGACCTTTATAGACACCAACGACTTCATACAGGGGAGAGACCCTATGAATGCACTGTATGTAAAAAGCGATTCACTCGGCGGTCACATCTTATAGGGCACCAGAGAACCCATTCTGAAGAAGAAACATATAAATGTCTTGAGTGTGGGAAAAGTTTTTGTCATGGATCAAGTCTTAAAAGACATCTGAAAACTCATACAGGTGAAAAACCTCATAGATGTCATAATTGTGGGAAAAGTTTTAGTCGACTGACAGCTCTTACTTTGCACCAGAGAACGCATACTGAAGAGAGACCTTTTAAATGTAATTATTGTGGGAAAAGTTTTAGACAGAGACCAAGCCTCGTTATTCATTTAAGAATCCACACAGGGGAGAAGCCATACAAGTGTACTCATTGTTCTAAAAGCTTCAGACAGAGAGCCGGCCTTATTATGCACCAGGTCACTCACTTTAGAGGACTTATTTAA ->chimp -ATGGCTGTGGCCCTGGGTTGTGCAATCCAGGCATCCTTGAATCAAGGCTCTGTGTTTCAAGAATATGATACTGACTGTGAAGTTTTCCGTCAGCGCTTCAGGCAGTTCCAGTACAGAGAAGCAGCTGGGCCTCATGAAGCATTTAACAAACTCTGGGAACTTTGCTGTCAATGGCTGAAGCCAAAGATGCGCTCTAAGGAACAAATCCTGGAGCTGCTAGTGTTGGAGCAATTCCTAACTATCCTGCCCACAGAGATAGAGACCTGGGTGAGGGAGCACTGCCCAGAGAATAGAGAAAGAGTTGTGTCACTGATAGAAGACTTACAGAGAGAACTTGAGATACCAGAGCAGCAG?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GATATCCATTACCCAAACTTGACATGAACTTCTCATTGGAGAATAGAGAAGAGCCATGGGTGAAGGAATTACAGGATTCTAAAGAAATGAAACAATTACTTGATTCCAAGATAGGTTTTGAGATCGGGATAGAAAATGAAGAAGATACTTCAAAACAGAAAAAAATGGAGACTATGTATCCATTTATTGTAACTTTAGAGGGGAATGCTCTCCAGGGTCCCATTTTGCAAAAAGACTATGTACAGTTAGAAAATCAATGGGAAACCCCCCCAGAGGATTTACAGAGAGATTTAGCAAAACTGGTAGATCAGCAGAACCCCACTCTGGGAGAGACACCTGAGAACTCCAACTTGGAAGAACCTCTCAACCCTAAACCCCACAAGAAAAAGAGTCCAGGAGAGAAACCTCACCGATGTCCTCAGTGTGGAAAATGTTTTGCTCGGAAGTCACAACTTACTGGGCATCAGAGAATTCATTCAGGAGAAGAACCTCACAAATGCCCTGAATGTGGGAAAAGATTCCTTCGTAGTTCAGACCTTTATAGACACCAACGACTTCATACAGGGGAGAGACCCTATGAATGCACTGTATGTAAAAAGCGATTCACTCGGCGGTCACATCTTATAGGGCACCAGAGAACCCATTCTGAAGAAGAAACATATAAATGTCTTGAGTGTGGGAAAAGTTTTTGTCATGGATCAAGTCTTAAAAGACATCTGAAAACTCATACAGGTGAAAAACCTCATAGATGTCATAATTGTGGGAAAAGTTTTAGTCGACTGACAGCTCTTACTTTGCACCAGAGAACGCATACTGAAGAGAGACCTTTTAAATGTAATTATTGTGGGAAAAGTTTTAGACAGAGACCAAGCCTCGTTATTCATTTAAGAATCCACACAGGGGAGAAGCCATACAAGTGTACTCATTGTTCTAAAAGCTTCAGACAGAGAGCCGGCCTTATTATGCACCAGGTCACTCACTTTAGAGGACTTATTTAA ->mouse -ATGGCTGTGGCCCTGGGCTGTGCAATCCAGGCCTCCTTGAATCAGGGCTCTGTGCTGCAAGAGTATGACACAGACTGTGAAGTTTTCCGACAGCGTTTCAGGCAGTTCCAGTACACAGAAGCTGCCGGGCCTCATGAAGCATTCAACAAACTCTGGGAGCTTTGCTGTCAGTGGCTGAAGCCAAAGATGCGTTCTAAGGAACAAATCCTGGAACTGCTTGTGCTAGAGCAATTCCTAACTATTCTGCCCACAGAAATAGAGACCTGGGTGAGGGAACACTGCCCAGACAATAGAGAAAGAGTTGTGTCACTCATTGAAGACTTACAAAGAGAGCTTGAGATACCAGAACCACAGATTGACATGGATGACATGCTCTTGGAAGAACTGGCGCCAGTTGGAACAGTACCCATGCCACCCAACTTGCACCTGGAGGAGCCTTCACTCCAGGTGATGGAACCTGTTCAGGAGCCTCCGGTGCCGGATGCCTGGATTCCACAAGCTGGCCCCCAGGATCTGAACTACAGTGCTGATGCTGAATGCCAGTCCTTTCTGGACCCTGGTTATCAGTTACCAAAGCTTGACATGAACTTCCCATTGGATCATAGAGAAGAACCATGGGTAAAAGACTTAGAGGATCCCAAAGAAATGAAACAATTACTTGATTCCAAGATTGGTTTTGAGATGGGAATAGAAAATGAAGAAGATACTTCAAAGGAAAAAAAACTGGAAACTTTGTACCCATTTGTTGTAACTTTAGAAGGGAATGCTCTCCATGGTCCCATTTTGCAGAAAGACTATGTGCAGTTAGAAAACCAATGGGAAACATCCCCAGAGGACTTACAGACAGACCTAACAAAACTCGTAGATCCTCAGAACCCAACTCTAGGAGAGACACCCGAGAGCCCCAGCCTGGAAGAACCTCTCACCCCGAAGCCTCCAAAGAAAAAGAGTCCTGGGGACAAACCTCACCGATGTCCCCAGTGTGGCAAATGTTTCGCTCGGAAGTCACAACTTACAGGGCACCAGCGAATTCATTCAGGAGAAGAACCTCACAAGTGCCCTGAATGCGGAAAAAGGTTCCTGCGTAGCTCTGACCTTTACAGACACCAACGACTTCACACAGGAGAAAGACCCTATGAATGCACTGTATGTAAAAAGCGATTCACTAGGCGCTCACACCTTCTTGGGCACCAGAGAACCCATTCTGAAGAAGAAACATATAAATGTCTTGAGTGTGGAAAAACCTTTTGTCATGGGTCAAGTCTTAAAAGACATCTAAAAACTCATACAGGTGAAAAGCCTCATAGATGTCCTAATTGTGGGAAAAGTTTTAGTCGCCTGACGGCACTTACTTTGCACCAGAGAACACACACGGAAGAGAGACCTTTTAAATGTAGTTACTGTGGGAAAAGCTTTAGACAGAGACCAAGCCTTGTCATTCATTTAAGAATCCATACAGGGGAAAAGCCATACAAGTGTACTCATTGTTCTAAAAGCTTCCGGCAGAGAGCAGGCCTTATTATGCACCAGGTCACACACTTTAGAGGACTTCTTTAA - ->human -?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CTTCTAGGGACCTATTAAAAGAGTTCCCACAGCCCAAAAATCTTCTCAACAGTGTGATTGGAAGAGCCCTCGGCATCTCACATGCAAAAGACAAACTAGTCTACGTGCACACAAATGGACCGAAGAAAAAGAAAGTCACACTGCACATAAAATGGCCCAAGAGCGTGGAGGTAGAAGGCTATGGCAGCAAGAAGATCGATGCTGAGCGGCAGGCTGCAGCTGCAGCCTGCCAGCTGTTCAAGGGTTGGGGTCTGCTAGGTCCCCGGAATGAGTTGTTTGACGCAGCCAAATACCGAGTGCTAGCTGATCGCTTTGGCTCCCCTGCCGACAGCTGGTGGCGTCCGGAACCCACCATGCCCCCTACTTCCTGGCGGCAGCTGAATCCAGAGAGTATTCGACCAGGGGGACCTGGGGGCCTATCCCGCTCTTTAGGCCGGGAAGAAGAGGAGGACGAGGAGGAAGAGCTAGAAGAAGGGACCATAGATGTTACCGACTTCTTGTCCATGACCCAGCAGGATTCCCACGCTCCACTCAGGGACTCAAGGGGGAGTTCCTTTGAGATGACAGATGACGACAGTGCCATTAGGGCTCTGACCCAGTTTCCACTTCCCAAGAACCTTCTGGCCAAGGTGATTCAGATTGCAACGTCATCCTCCACAGCTAAGAACCTCATGCAGTTCCATACTGTGGGCACCAAGACCAAGCTGTCTACACTCACCCTGCTCTGGCCCTGCCCCATGACCTTTGTTGCCAAAGGGCGCCGCAAAGCAGAGGCTGAGAATAAGGCGGCAGCCTTGGCCTGCAAGAAACTGAAGAGCCTGGGCCTGGTGGACAGGAACAACGAACCGCTTACACACGCCATGTATAACCTGGCCTCTTTGCGTGAGCTGGGTGAGACCCAGCGCCGACCATGCACCATCCAGGTGCCCGAGCCCATCCTCCGCAAGATAGAGACCTTCCTGAACCATTACCCTGTGGAGAGTTCATGGATCGCCCCAGAACTCCGGCTGCAGAGTGATGACATCTTGCCCTTGGGCAAGGACTCAGGGCCTCTGAGTGACCCTATCACAGGCAAGCCCTATGTGCCCCTGTTGGAAGCAGAGGAGGTACGTCTCAGCCAGAGTCTGCTAGAACTGTGGCGGCGGCGAGGGCCGGTCTGGCAGGAGGCCCCCCAGCTACCTGTGGACCCACATCGGGACACCATCCTCAACGCCATTGAGCAGCACCCGGTGGTGGTCATCTCTGGGGACACGGGCTGTGGGAAGACCACGCGCATCCCCCAGCTGTTGCTGGAGCGCTATGTGACCGAGGGCCGAGGTGCCCGCTGCAATGTTATCATCACCCAACCTCGCCGCATCTCTGCTGTGTCTGTGGCACAGCGGGTCAGCCACGAACTGGGCCCCTCCCTGCGCCGGAATGTGGGCTTCCAGGTGCGGTTGGAAAGTAAGCCCCCATCCCGAGGCGGGGCCCTGCTCTTCTGCACTGTGGGTATCCTGCTGCGTAAGCTGCAGAGCAACCCCAGCCTGGAGGGCGTGAGCCACGTCATCGTGGATGAGGTGCATGAGCGGGACGTGAACACAGACTTTCTGCTGATCCTGCTCAAGGGCCTGCAGCGGCTCAACCCGGCCCTGCGGCTGGTGCTCATGAGTGCCACAGGGGACAATGAGCGCTTCTCCCGATACTTTGGTGGCTGCCCCGTCATCAAGGTGCCTGGCTTCATGTACCCAGTCAAGGAGCACTACCTAGAGGACATCCTGGCCAAGTTGGGCAAGCACCAGTACCTGCACCGGCACCGGCACCATGAGTCTGAGGATGAATGCGCACTCGATTTGGACCTTGTGACTGATCTGGTTCTGCACATCGATGCTCGCGGGGAACCAGGTGGGATCCTGTGCTTCCTGCCTGGGTGGCAGGAGATCAAAGGAGTGCAGCAGCGCCTCCAGGAGGCCCTGGGCATGCACGAGAGCAAGTACCTCATCCTGCCAGTGCACTCCAACATCCCCATGATGGATCAGAAGGCCATATTCCAGCAGCCTCCAGTTGGGGTGCGCAAGATTGTCTTGGCCACCAACATTGCTGAGACTTCCATCACAATCAATGACATCGTGCATGTGGTGGACAGTGGGCTGCACAAGGAAGAACGCTATGACCTGAAGACCAAGGTGTCCTGCCTGGAGACAGTGTGGGTATCAAGAGCCAATGTGATCCAGCGCCGGGGCCGGGCGGGCCGCTGCCAGTCCGGCTTTGCCTACCACTTGTTCCCTCGAAGCCGGCTGGAGAAAATGGTCCCTTTCCAAGTGCCAGAGATCCTGCGCACACCTCTTGAGAACCTGGTGCTGCAAGCGAAAATCCACATGCCTGAGAAGACGGCGGTGGAGTTCCTGTCCAAGGCTGTGGACAGTCCAAACATCAAGGCAGTGGACGAGGCTGTGATCTTGCTCCAGGAGATCGGGGTGCTGGACCAGCGGGAGTACCTGACTACCCTGGGGCAGCGCCTGGCTCACATCTCCACCGACCCCCGGTTGGCCAAGGCCATTGTGTTGGCTGCCATCTTCCGTTGCCTGCACCCACTACTGGTGGTCGTTTCCTGCCTCACCCGGGACCCCTTCAGCAGCAGCCTACAGAACCGGGCAGAGGTGGACAAGGTGAAAGCACTGTTGAGCCATGACAGCGGCAGTGACCACCTGGCCTTTGTGCGGGCTGTCGCCGGCTGGGAGGAGGTGCTGCGTTGGCAGGACCGCAGCTCCCGGGAGAATTACCTGGAGGAAAACCTGCTGTACGCACCCAGCCTGCGCTTCATCCACGGACTCATCAAGCAGTTCTCAGAGAACATTTATGAGGCCTTCCTGGTGGGGAAGCCCTCGGACTGCACCCTGGCCTCCGCCCAGTGCAACGAGTACAGTGAGGAGGAGGAGCTGGTGAAGGGCGTGCTGATGGCCGGCCTCTACCCCAACCTCATCCAGGTGAGGCAGGGCAAGGTCACCCGGCAGGGGAAGTTCAAGCCCAACAGCGTCACATATAGGACCAAATCAGGCAACATCCTGCTGCACAAGTCGACCATTAACAGGGAGGCCACACGGTTACGGAGCCGATGGCTGACGTATTTCATGGCAGTCAAGTCCAATGGCAGCGTCTTCGTCCGGGACTCCTCTCAGGTGCACCCGCTAGCTGTGCTGCTGCTGACCGACGGGGACGTGCACATCCGTGATGACGGGCGCCGGGCCACCATCTCACTGAGCGACAGTGACCTGCTGCGGCTGGAGGGTGACTCGCGTACCGTGCGGCTGCTGAAGGAGCTGCGGCGGGCCCTGGGCCGCATGGTGGAGCGGAGCCTGCGCAGCGAGCTGGCTGCACTTCCCCCCAGCGTACAGGAGGAGCACGGGCAGCTGCTTGCGCTACTGGCAGAGCTGCTGCGAGGACCCTGTGGCAGCTTTGATGTGCGCAAGACAGCTGACGACTGA ->chimp -????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????AAAGTCACACTGCACATAAAGTGGCCCAAGAGCGTGGAGGTAGAAGGCTATGGCAGCAAGAAGATCGATGCTGAGCGGCAGGCTGCAGCTGCGGCCTGCCAGCTGTTCAAGGGTTGGGGTCTG??AGGTCCCCGGAATGAGTTGTTTGACGCAGCCAAATACCGAGTGCTAGCTGATCGCTTTGGCTCCCCTGCCGACAGCTGGTGGCGTCCGGAACCCACCATGCCCCCTACTTCCTGGCGGCAGCTGAATCCAGAGAGTATTCGACCAGGGGGACCTGGGGGCCTATCCCGCTCTTTAGGCCGGGAAGAAGAGGAGGACGAGGAGGAAGAGCTAGAAGAAGGGACCATAGATGTTACCGACTTCTTGTCCATGACCCAGCAGGATTCCCACGCTCCACTCAGGGACTCAAGGGGGAGTTCCTTTGAGATGACAGATGACGACAGTGCCATTAGGGCTCTGACCCAGTTTCCACTTCCCAAGAACCTTCTGGCCAAGGTGATTCAGATTGCAACGTCATCCTCCACAGCTAAGAACCTCATGCAGTTCCATACTGTGGGCACCAAGACCAAGCTGTCTACACTCACCCTGCTCTGGCCCTGCCCCATGACCTTTGTTGCCAAAGGGCGCCGCAAAGCAGAGGCTGAGAATAAGGCGGCAGCCTTGGCCTGCAAGAAACTGAAGAGCCTGGGCCTGGTGGACAGGAACAACGAACCGCTTACACACGCCATGTATAACCTGGCCTCTTTGCGTGAGCTGGGTGAGACCCAGCGCCGACCATGCACCATCCAGGTGCCCGAGCCCATCCTCCGCAAGATAGAGACCTTCCTGAACCATTACCCTGTGGAGAGTTCATGGATCGCCCCAGAACTCCGGCTGCAGAGTGATGACATCTTGCCCTTGGGCAAGGACTCAGGGCCTCTGAGTGACCCTATCACAGGCAAGCCCTATGTGCCCCTGTTGGAAGCAGAGGAGGTACGTCTCAGCCAGAGTCTGCTAGAACTGTGGCGGCGGCGAGGGCCGGTCTGGCAGGAGGCCCCCCAGCTACCTGTGGACCCACATCGGGACACCATCCTCAACG?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CCTCCCTGCGCCGGAATGTGGGCTTCCAGGTGCGGTTGGAAAGTAAGCCCCCATCCCGAGGCGGGGCCCTGCTCTTCTGCACTGTGGGTATCCTGCTGCGTAAGCTGCAGAGCAACCCCAGCCTGGAGGGCGTGAGCCACGTCATCGTGGATGAGGTGCATGAGCGGGACGTGAACACAGACTTTCTGCTGATCCTGCTCAAGGGCCTGCAGCGGCTCAACCCGGCCCTGCGGCTGGTGCTCATGAGTGCCACAGGGGACAATGAGCGCTTCTCCCGATACTTTGGTGGCTGCCCCGTCATCAAGGTGCCTGGCTTCATGTACCCAGTCAAGGAGCACTACCTAGAGGACATCCTGGCCAAGTTGGGCAAGCACCAGTACCTGCACCGGCACCGGCACCATG?????????????????????????????????????????????????????????????????????????????????????????????????????????GGCAGGAGATCAAAGGAGTGCAGCAGCGCCTCCAGGAGGCCCTGGGCATGCACGAGAGCAAGTACCTCATCCTGCCAGTGCACTCCAACATCCCCATGATGGATCAGAAGGCCATATTCCAGCAGCCTCCAGTTGGGGTGCGCAAGATTGTCTTGGCCACCAACATTGCTGAGACTTCCATCACAATCAATGACATCGTGCATGTGGTGGACAGTGGGCTGCACAAGGAAGAACGCTATGACCTGAAGACCAAGGTGTCCTGCCTGGAGACAGTGTGGGTATCAAGAGCCAATGTGATCCAGCGCCGGGGCCGGGCGGGCCGCTGCCAGTCCGGCTTTGCCTACCACTTGTTCCCTCGAAGCCGGCTGGAGAAAATGGTCCCTTTCCAAGTGCCAGAGATCCTGCGCACACCTCTCGAGAACCTGGTGCTGCAAGCAAAAATCCACATGCCTGAGAAGACGGCGGTGGAGTTCCTGTCCAAGGCTGTGGACAGTCCAAACATCAAGGCAGTGGACGAGGCTGTGATCTTGCTCCAGGAGATCGGGGTGCTGGACC??CGGGAGTACCTGACTACCCTGGGGCAGCGCCTGGCTCACATCTCCACCGACCCCCGGTTGGCCAAGGCCATTGTGTTGGCTGCCATCTTCCGTTGCCTGCA???ACTACTGGTG????TTTCCTGCCTCACCCGGGACCCCTTC????????????????????????????????????GTGAAAGCACTG?TGAGCCATGACAGCGGCAGTGACCACCTGGCCTTTGTGCGGGCTGTCGCCGGCTGGGAGGAGGTGCTGCGTTGGCAGGACCGCAGCTCCCGGGAGAATTACCTGGAGGAAAACCTGCTCTACGCACCCAGCCTGCGCTTCATCCACGGACTCATCAAGCAGTTCTCAGAGAACATTTATGAGGCCTTCCTGGTGGGGAAGCCCTCGGACTGCACCCTGGCCTCCGCCCAGTGCAACGAGTACAGTGAGGAGGAGGAGCTGGTGAAGGGCGTGCTGATGGCCGGCCTCTACCCCAACCTCATCCAGGTGAGGCAGGGCAAGGTCACCCGGCAGGGGAAGTTCAAGCCCAACAGCGTCACATATAGGACCAAATCAGGCAACATCCTGCTGCACAAGTCGACCATTAACAGGGAGGCCACACGGTTACGGAGCCGATGGCTGACGTATTTCATGGCAGTCAAGTCCAATGGCAGCGTCTTCGTCCGGGACTCCTCTCAGGTGCACCCGCTAGCTGTGCTGCTGCTGACCGACGGGGACGTGCACATCCGTG?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->mouse -?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CTTCTAGGGACCTATTAAAAGAGTTTCCGCAGCCTAAAAACCTTCTCAACAGCGTGATTGGAAGAGCCCTTGGCATCTCACATGCAAAAGACAAGTTAGTCTATGTGCACACGAATGGACCGAAGAAAAAGAAAGTCACCCTGCACATAAAGTGGCCCAAGAGCGTGGAGGTGGAAGGCTATGGCAGCAAGAAGATTGATGCTGAGCGTCAGGCTGCAGCAGCTGCCTGCCAACTCTTCAAGGGCTGGGGTCTGCTGGGACCACGGAATGAGCTGTTTGATGCAGCTAAATACCGAGTGCTAGCTGATCGTTTTGGGTCTCCAGCTGACAGCTGGTGGCGCCCAGAACCCACCATGCCTCCAACTTCCTGGCGGCAGCTGAATCCTGAGAACATTCGGCCAGGGGGTCCTGCAGGACTATCCCGATCCTTAGGCCGAGAGGAAGAGGAAGATGAGGAGGAAGAGCTAGAAGAGGGGACCATTGATGTGACAGAGTTTCTGTCTATGACCCAGCAAGACTCCCACAACCCACTCAGGGACTCAAGGGGGGGCTCCTTTGAAATGACAGATGATGACAGTGCTATCAGAGCTCTGACCCAGTTTCCACTTCCCAAGAACCTCCTGGCCAAAGTGATTCAGATTGCAACCTCCTCCTCCACAGCTAAGAATCTCATGCAGTTCCATACTGTGGGTACCAAGACCAAGCTGGCTACACTCACTCTGCTCTGGCCCTGTCCCATGACCTTTGTTGCCAAAGGGCGACGCAAAGCTGAGGCTGAGAATAAGGCAGCAGCCTTGGCTTGCAAGAAACTGAAGAGCCTTGGCCTTGTGGACAGGAACAATGAGCCGCTTACCCATGCCATGTACAACCTGGCCTCCCTGCGTGAGTTGGGTGAGACCCAGCGCCGGCCATGTACCATCCAGGTGCCTGAGCCCATCCTTCGCAAGATAGAGGCCTTCCTGAGTCATTACCCGGTGGACAGCTCATGGATTTCCCCAGAACTCCGACTGCAGAGTGATGACATCTTGCCCTTAGGCAAGGACTCAGGGCCCTTGAGTGACCCTATCACAGGCAAGCCATACATGCCCCTGTCAGAAGCAGAGGAGGTGCGCTTAAGCCAGAGCCTGCTAGAGCTGTGGCGGAGGAGAGGGCCGATCTGGCAGGAGGCCCCGCAGCTACCTGTAGACCCTCATCGGGACACTATCCTCAGTGCCATTGAACAACACCCAGTGGTAGTCATCTCTGGGGACACAGGCTGTGGGAAGACCACACGTATCCCTCAGCTGCTATTGGAGCGCTATGTGACTGAGGGTCGAGGTGCCCGCTGCAATGTGATCATCACACAACCTCGCCGGATCTCAGCTGTGTCTGTGGCACAGCGGGTCAGCCATGAACTGGGCCCCTCCTTGCGCCGGAATGTGGGCTTCCAGGTACGCTTGGAAAGTAAGCCCCCAGCCCGAGGTGGGGCGCTGCTCTTCTGCACTGTGGGTATCCTGCTTCGGAAGCTGCAGAGCAACCCCAGCCTGGAGGGTGTGAGCCATGTCATTGTGGATGAGGTCCATGAGCGGGATGTGAACACAGACTTCCTGCTGATTCTGCTCAAGGGCCTGCAGCGGCTCAACCCAGCTCTTCGGCTGGTGCTCATGAGTGCTACAGGAGATAATGAGCGCTTTTCCCGATACTTTGGGGGCTGCCCTGTTATCAAGGTACCTGGCTTCATGTATCCCGTCAAGGAACACTACCTGGAGGACATCTTGGCCAAGCTGGGTAAACATCAGTACCCACACCGGCATTGGCACCATGAGTCGGAAGATGAATGTGCACTTGATTTGGACCTTGTGACTGACCTGGTTCTGCATATCGATGCCCGTGGGGAACCAGGTGGGATCCTGTGCTTTCTACCTGGCTGGCAAGAAATCAAAGGAGTGCAACAACGGCTCCAGGAGGCCCTGGGCATGCATGAAAGCAAGTACCTCATCTTACCAGTGCACTCCAATATCCCCATGATGGACCAGAAGGCCATATTCCAACAGCCTCCACTTGGGGTACGCAAGATTGTATTGGCCACCAACATTGCTGAAACCTCCATCACAGTTAACGACATTGTACATGTCGTGGACAGCGGTCTGCACAAGGAGGAACGCTATGACCTGAAGACCAAGGTGTCCTGCCTGGAGACTGTGTGGGTGTCGAGAGCAAATGTCATTCAGCGCCGGGGCAGGGCAGGCCGCTGCCAGTCAGGTTTTGCCTACCACTTGTTCCCGAGGAGCCGGCTGGAGAAAATGGTTCCTTTCCAAGTGCCAGAGATCCTGCGCACACCTCTTGAGAACCTGGTGCTGCAAGCCAAAATCCATATGCCTGAGAAGACGGCAGTGGAGTTCCTCTCTAAGGCTGTGGACAGTCCAAATATCAAGGCAGTGGATGAGGCCGTGATCCTGCTCCAGGAGATTGGGGTGCTGGACCAGCGGGAGTATCTGACCACCTTGGGACAGCGCCTGGCCCACATCTCTACTGACCCCCGACTGGCCAAGGCCATAGTGTTGGCTGCCATCTTCCGTTGCCTGCACCCACTGCTGGTGGTTGTTTCCTGCCTTACCCGGGACCCCTTCAGCAGCAGTTTGCAGAACCGGGCAGAAGTAGACAAGGTGAAGGCATTGCTGAGCCATGACAGTGGCAGTGACCATTTGGCCTTCGTGCGGGCTGTGGCTGGCTGGGAGGAGGTACTGCGCTGGCAGGACCGTACCTCCAGGGAAAACTACCTGGAAGAAAACCTTCTGTATGCCCCCAGCTTGCGCTTCATCCACGGGCTCATCAAGCAGTTCTCAGAGAACATTTATGAGGCTTTCCTAGTGGGGAAGCCCTCTGACTGCACACTGCCCTCTGCTCAGTGCAATGAGTACAGCGAGGAAGAGGAGCTGGTGAAGGGTGTGCTGATGGCTGGCCTCTACCCCAACCTCATCCAGGTGAGACAAGGTAAGGTTACTCGGCAAGGCAAGTTCAAACCCAACAGTGTCACTTACAGGACCAAATCTGGCAACATCTTGCTGCATAAGTCAACCATTAACAGGGAGGCTACCCGGTTACGGAGCCGATGGCTGACATATTTCATGGCCGTCAAGTCCAATGGTAGCGTCTTTGTTCGAGATTCCTCCCAGGTGCACCCACTAGCTGTGTTGCTCCTAACAGATGGGGACGTGCACATCCGAGATGATGGGCGTCGGGCCACCATCTCATTGAGTGACAGCGACCTGCTTCGGCTGGAAGGTGATTCACGAACTGTGCGGTTGCTAAGGGAGTTTCGTCGAGCCCTAGGACGGATGGTGGAGCGGAGCCTCCGCAGCGAGTTAGCTGCACTTCCTCTTAGTGTGCAGCAAGAACACGGGCAGCTGCTTGCACTGCTGGCAGAGTTGCTTCGAGGACCTTGTGGCAGCTTTGATATGCGCAAGACAGCTGATGACTGA - ->human -ATGGAAAACGAGACAGTCAGTGAACTGAACCAAACACAGCTTCAGCCACGAGCAGTGGTGGCCTTAGAATACCAGGTGGTCACCATCTTACTTGTACTCATTATTTGTGGCCTGGGCATTGTAGGCAACATCATGGTAGTCCTGGTTGTCATGAGAACCAAGCACATGAGGACCCCCACAAACTGCTACCTGGTGAGCCTGGCAGTAGCTGATCTCATGGTCTTGGTGGCCGCAGGCCTCCCCAACATAACAGACAGTATCTACGGTTCCTGGGTCTATGGCTATGTTGGATGCCTCTGCATTACTTACCTCCAGTATTTGGGAATTAATGCATCCTCTTGTTCAATAACAGCCTTTACCATTGAGAGGTACATAGCAATCTGTCACCCCATCAAAGCCCAGTTTCTCTGCACATTTTCCAGAGCCAAAAAGATTATCATCTTTGTCTGGGCTTTCACATCTCTTTACTGTATGCTCTGGTTCTTCTTGCTGGATCTCAATATTAGCACCTACAAAGATGCTATTGTGATATCCTGTGGCTACAAGATCTCCAGGAATTACTACTCACCTATTTACCTAATGGACTTTGGTGTCTTTTATGTTGTGCCAATGATCCTGGCTACCGTCCTCTATGGATTCATAGCTAGAATCCTTTTCTTAAATCCCATTCCTTCAGATCCTAAAGAAAACTCTAAGACATGGAAAAATGATTCAACCCATCAGAACACAAATCTGAATGTAAATACCTCTAATAGATGTTTCAACAGCACAGTATCTTCAAGGAAGCAGGTCACCAAGATGCTGGCAGTGGTTGTAATTCTGTTTGCCCTTTTATGGATGCCCTACAGGACTCTAGTGGTTGTCAACTCATTTCTCTCCAGTCCTTTCCAAGAAAATTGGTTTTTGCTCTTTTGCAGAATTTGCATTTATCTCAACAGTGCCATCAACCCGGTGATTTACAATCTCATGTCCCAGAAATTCCGTGCAGCCTTCAGAAAGCTCTGCAACTGCAAGCAGAAGCCAACAGAGAAACCTGCTAACTACAGTGTGGCCCTAAATTACAGCGTCATCAAGGAGTCAGACCATTTCAGCACAGAGCTTGATGATATCACTGTCACTGACACTTACCTGTCTGCCACAAAAGTGTCTTTTGATGACACCTGCTTGGCTTCTGAGGTATCCTTTAGCCAAAGTTGA ->chimp -ATGGAAAACGAGACAGTCAGTGAACTGAACCAAACACAGCTTCAGCCACGAGCAGTGGTGGCCTTAGAATACCAGGTGGTCACCATCTTACTTGTGCTCATTATTTGTGGCCTGGGCATTGTAGGCAACATCATGGTAGTCCTGGTTGTCATGAGAACCAAGCACATGAGGACCCCCACAAACTGCTACCTGGTGAGCCTGGCAGTAGCTGATCTCATGGTCTTGGTGGCCGCAGGCCTCCCCAACATAACAGACAGTATCTACGGTTCCTGGGTCTATGGCTATGTTGGATGCCTCTGCATTACTTACCTCCAGTATTTGGGAATTAATGCATCCTCTTGTTCAATAACAGCCTTTACCATTGAGAGGTACATAGCAATCTGTCACCCCATCAAAGCCCAGTTTCTCT????ATTTTCCAGAGCCAAAAAGATTATCATTTTTGTTTGGGCTTTCACATCTCTTTACTGTATGCTCTGGTTCTTCTTGCTGGATCTCAATATTAGCACCTACAAAGATGCTATTGTGATATCCTGTGGCTACAAGATCTCCAGGAATTACTACTCACCTATTTACCTAATGGACTTTGGTGTCTTTTATGTTGTGCCAATGATCCTGGCTACCGTCCTCTATGGATTCATAGCTAGAATCCTTTTCTTAAATCCCATTCCTTCAGATCCTAAAGAAAACTCTAAGACATGGAAAAATGACTCAACCCATCAGAACACAAATTTGAATGTAAATACTTCTAATAGATGTTTCAACAGCACAGTATCTTCAAGGAAGCAGGTCACCAAGATGCTGGCAGTGGTTGTAATTCTGTTTGCCCTTTTATGGATGCCCTACAGGACTCTGGTGGTTGTCAACTCATTTCTCTCCAGTCCTTTCCAAGAAAATTGGTTTTTGCTCTTTTGCAGAATTTGCATTTATCTCAACAGTGCCATCAACCCGGTGGTTTACAATCTCATGTCCCAGAAATTCCGTGCAGCCTTCAGAAAGCTCTGCAACTGCAAGCAGAAGCCAACAGAGAAACCTGCTAACTACAGTGTGGCCCTAAATTACAGCGTCATCAAGGAGTCAGACCATTTCAGCACAGAGCTTGATGATATCACTGTCACTGACACTTACCTGTCTGCCACAAAAGTGTCTTTTGATGACACCTGCTTGGCTTCTGAGGTATCCTTTAGCCAAAGTTGA ->mouse -ATGGAGAATGATACTGTCAGTGAAATGAACCAAACCGAGCTCCAGCCACAAGCAGCTGTGGCCCTCGAGTACCAGGTGGTTACCATCTTACTTGTGGTCATTATTTGTGGACTGGGCATTGTGGGCAACATCATGGTAGTCCTGGTGGTCATGAGAACAAAGCACATGAGAACCCCTACAAACTGTTACCTGGTAAGTCTGGCTGTGGCAGATCTCATGGTTCTGGTGGCTGCAGGCCTCCCCAACATAACCGACAGTATCTATGGTTCCTGGGTCTATGGCTATGTTGGCTGCCTCTGCATTACATATCTCCAGTACCTAGGCATTAATGCATCTTCATGTTCAATAACGGCCTTTACCATTGAAAGGTACATAGCAATCTGTCACCCCATCAAAGCCCAGTTTCTCTGCACGTTTTCCAGAGCCAAAAAAATCATCATCTTTGTCTGGGCCTTCACATCCATTTACTGTATGCTCTGGTTCTTCCTGCTGGATCTCAACATCAGCACCTACAAAAACGCTGTTGTGGTTTCCTGTGGCTACAAGATCTCCAGGAACTACTACTCACCTATTTACCTAATGGACTTTGGTGTCTTTTATGTTGTGCCAATGATCCTGGCCACTGTGCTTTATGGATTTATAGCTAGAATCCTCTTCTTAAACCCCATTCCTTCAGACCCTAAAGAAAACTCTAAGATGTGGAAAAATGACTCAATCCATCAGAACAAGAATTTGAATTTAAATGCCACCAACAGATGCTTCAACAGCACTGTATCTTCCAGGAAGCAGGTCACCAAGATGCTCGCAGTGGTTGTAATTCTGTTTGCCCTTTTATGGATGCCCTACAGGACTCTTGTGGTTGTCAACTCATTTCTCTCCAGCCCTTTCCAGGAAAATTGGTTCTTGCTCTTTTGCAGAATTTGCATTTATCTCAACAGTGCCATCAACCCAGTGATTTACAACCTCATGTCTCAGAAATTTCGTGCAGCCTTCAGGAAGCTCTGCAATTGCAAGCAGAAGCCCACAGAAAAAGCTGCTAACTACAGTGTGGCCCTAAATTACAGTGTCATCAAGGAGTCAGACCGCTTCAGCACAGAGCTAGAAGATATCACCGTCACCGATACGTATGTGTCAACCACAAAAGTGTCCTTTGATGACACCTGCTTGGCCTCTGAGGTAACCTTTAGTCAGAGCTGA - ->human -ATGACTGAGTTCTGGCTTATATCTGCTCCTGGGGAGAAAACCTGTCAGCAAACATGGGAGAAATTGCATGCGGCAACTTCAAAGAACAATAATCTTGCTGTCACTTCCAAGTTCAATATTCCTGACTTAAAGGTTGGCACGTTGGATGTCTTGGTTGGCTTGTCAGATGAACTGGCTAAACTGGATGCATTTGTAGAAGGAGTGGTTAAGAAAGTAGCTCAATACATGGCTGATGTATTGGAAGATAGCAAAGACAAAGTTCAAGAGAATCTGTTGGCTAATGGAGTGGACTTGGTTACTTATATAACAAGGTTCCAGTGGGACATGGCCAAATATCCAATCAAGCAGTCCCTGAAAAATATTTCTGAAATAATTGCCAAGGGAGTAACTCAGATTGATAATGACCTGAAATCTCGAGCATCTGCATACAATAACCTGAAAGGAAATCTTCAGAATTTGGAACGAAAGAATGCAGGAAGTTTGCTAACTAGAAGTCTAGCAGAAATTGTGAAGAAGGATGACTTTGTTCTTGATTCAGAGTATCTCGTCACATTACTGGTAGTAGTTCCCAAGTTAAACCACAACGACTGGATTAAGCAGTATGAAACACTAGCCGAAATGGTAGTTCCAAGGTCTAGCAATGTTCTTTCAGAGGACCAAGACAGTTACCTGTGTAATGTCACCTTGTTTAGGAAGGCAGTTGATGACTTCAGACACAAAGCCAGAGAAAACAAATTCATTGTTCGTGACTTCCAGTATAATGAAGAGGAGATGAAAGCAGATAAAGAAGAAATGAACAGGCTTTCTACTGATAAGAAAAAACAATTTGGACCACTTGTACGGTGGCTGAAAGTGAATTTTAGTGAAGCATTTATTGCATGGATTCACGTGAAAGCATTACGGGTTTTCGTTGAGTCTGTTTTAAGGTATGGCTTGCCAGTGAACTTCCAAGCAATGCTACTTCAGCCCAATAAGAAAACTTTGAAGAAACTGAGAGAAGTATTACATGAATTGTATAAACATCTAGACAGCAGTGCAGCAGCTATTATTGATGCTCCTATGGATATTCCAGGTTTAAACCTGAGTCAACAAGAATACTACCCCTATGTGTACTACAAGATTGATTGCAACTTGCTGGAATTCAAGTGA ->chimp -ATGACTGAGTTCTGGCTTATATCTGCTCCTGGGGAGAAAACCTGTCAGCAAACATGGGAGAAATTGCATGCGGCAACTTCAAAGAACAATAATCTTGCTGTCACTTCCAAGTTCAATATTCCTGACTTAAAGGTTGGCACGTTGGATGTCTTGGTTGGCTTGTCAGATGAACTGGCTAAACTGGATGCATTTGTAGAAGGAGTGGTTAAGAAAGTAGCTCAATACATGGCTGATGTATTGGAAGATAGCAAAGACAAAGTTCAAGAGAATCTGTTGGCTAATGGAGTGGACTTGGTTACTTATATAACAAGGTTTCAGTGGGACATGGCCAAATATCCAATCAAGCAGTCCCTGAAAAATATTTCTGAAATAATTGCCAAGGGAGTAACTCAGATTGATAATGACCTGAAATCTCGAGCATCTGCATACAATAACCTGAAAGGAAATCTTCAGAATTTGGAACGAAAGAATGCAGGAAGTTTGCTAACTAGAAGTCTAGCAGAAATTGTGAAGAAGGATGACTTTGTTCTTGATTCAGAGTATCTCGTCACATTACTGGTAGTAGTTCCCAAGTTAAACCACAACGACTGGATTAAGCAGTATGAAACACTAGCCGAAATGGTAGTTCCAAGGTCTAGCAATGTTCTTTCAGAGGACCAAGACAGTTACCTGTGTAATGTCACCTTGTTTAGGAAGGCAGTTGATGACTTCAGACACAAAGCCAGAGAAAACAA??????????????????????????ATGAAGAGGAGATGAAAGCAGATAAAGAAGAAATGAACAGG???TCTACTGATAAGAAAAAACAATTTGGACCACTTGTACGGTGGCTGAAAGTGAATTTTAGTGAAGCATTTATTGCATGGATTCACGTGAAAGCATTACGGGTTTTCGTTGAGTCTGTTTTAAGGTATGGCTTGCCAGTGAACTTCCAAGCAAT?CTACTTCAGCCCAATAAGAAAACTTTGAAGAAACTGAGAGAAGTATTACATGAATTGTATAAACATCTAGACAGCAGTGCAGCAGCTATTATTGATGCTCCTATGGATATTCCAGGTTTAAACCTGAGTCAACAAGAATACTACCCCTATGTGTACTACAAGATTGATTGCAACTTGCTGGAATTCAAGTGA ->mouse -ATGACTGAGTTCTGGCTCATATCTGCTCCTGGGGAGAAAACCTGTCAGCAAACATGGGAGAAACTACATGCAGCGACCACCAAGAACAATAATCTTGCCGTCTCTTCCAAGTTCAACATTCCTGACCTAAAGGTTGGCACGTTGGATGTCTTGGTTGGCTTGTCGGATGAACTGGCTAAACTGGATGCATTTGTAGAAGGTGTGGTCAAGAAAGTGGCTCAGTACATGGCTGATGTGCTGGAGGACAGCAAAGATAAAGTTCAGGAGAACTTGCTGGCCAGCGGAGTTGACTTGGTTACTTACATAACAAGGTTCCAGTGGGATATGGCTAAATATCCAATCAAGCAGTCTCTGAAAAATATTTCTGAAATAATTGCCAAGGGAGTGACTCAGATCGATAATGACCTAAAGTCTCGGGCGTCTGCATACAATAACCTGAAAGGGAATCTTCAGAATTTAGAGCGAAAGAACGCGGGAAGTTTGCTAACGCGAAGCCTGGCGGAAATCGTGAAGAAAGATGACTTTGTTCTTGATTCGGAGTATCTTGTCACATTGCTGGTGGTAGTTCCCAAGCTGAACCACAATGACTGGATTAAGCAGTATGAAACGCTCGCAGAAATGGTAGTACCAAGGTCAAGCAATGTTCTTTCAGAGGACCAAGACAGTTATCTTTGTAACGTCACCTTGTTTAGAAAAGCAGTTGATGATTTCAGACACAAAGCCAGAGAAAACAAGTTCATAGTTCGTGACTTCCAGTATAACGAGGAGGAGATGAAAGCAGATAAAGAAGAAATGACCAGGCTGTCTACTGACAAGAAGAAGCAGTTTGGACCACTTGTGCGGTGGCTTAAAGTGAATTTCAGTGAGGCGTTTATTGCGTGGATTCATATAAAAGCATTACGGGTTTTTGTGGAGTCTGTTTTAAGGTATGGCTTGCCGGTGAACTTCCAAGCAATGCTCCTTCAGCCGAATAAGAAGTCAGTGAAGAAGCTAAGAGAAGTGCTGCACGAGTTGTACAAGCATCTGGACAGCAGTGCGGCTGCCATCATTGACGCTCCCATGGATATCCCTGGCCTAAACCTGAGTCAGCAGGAATACTACCCCTATGTGTATTACAAGATTGATTGCAACTTGCTGGAATTCAAGTAA - ->human -ATGCCTTCCAGCGGCAGAGCGCTGCTGGACTCGCCG---CTGGACAGCGGCTCCCTGACCTCCCTGGACTCTAGTGTCTTCTGCAGCGAGGGTGAAGGGGAGCCCTTGGCGCTCGGGGACTGCTTCACGGTCAACGTGGGCGGCAGCCGCTTCGTGCTCTCGCAGCAGGCGCTGTCCTGCTTCCCGCACACGCGCCTTGGCAAGCTGGCCGTGGTGGTGGCTTCCTACCGCCGCCCCGGGGCCCTGGCCGCCGTGCCCAGCCCTCTGGAGCTTTGCGACGATGCCAACCCCGTGGACAACGAGTACTTCTTCGACCGCAGCTCGCAGGCGTTCCGATATGTCCTGCACTACTACCGCACCGGCCGCCTGCATGTCATGGAGCAGCTGTGCGCGCTCTCCTTCCTGCAGGAGATCCAGTACTGGGGCATCGATGAGCTCAGCATCGATTCCTGCTGCAGGGACAG????????????????????????????????????????????????????????????????????????????????????????????????????CCTTGTCCCACTGTTCGCCAGAAGCTCTGGAATATCCTGGAGAAACCTGGATCTTCCACAGCTGCCCGTATCTTTGGCGTCATCTCCATTATCTTCGTGGTGGTGTCCATCATTAACATGGCCCTGATGTCAGCTGAGTTAAGCTGGCTGGACCTGCAGCTGCTGGAAATCCTGGAGTATGTGTGCATTAGCTGGTTCACCGGGGAGTTTGTCCTCCGCTTCCTGTGTGTGCGGGACAGGTGTCGCTTCCTAAGAAAGGTGCCAAACATCATAGACCTCCTTGCCATCTTGCCCTTCTACATCACTCTTCTGGTAGAGAGCCTAAGTGGGAGCCAGACCACGCAGGAGCTGGAGAACGTGGGGCGCATTGTCCAGGTGTTGAGGCTGCTCAGGGCTCTGCGCATGCTAAAGCTGGGCAGACATTCCACAGGATTACGCTCCCTTGGGATGACAATCACCCAGTGTTACGAAGAAGTCGGCCTACTGCTCCTATTTCTATCCGTGGGAATCTCTATATTTTCAACTGTAGAATACTTTGCTGAGCAAAGCATTCCTGACACAACCTTCACAAGTGTCCCTTGTGCATGGTGGTGGGCCACCACCTCTATGACTACTGTGGGATATGGGGACATTAGACCAGACACCACCACAGGCAAAATCGTGGCCTTCATGTGTATATTATCGGGAATTCTTGTCTTGGCCTTGCCTATTGCTATTATTAACGATCGCTTCTCTGCTTGCTACTTCACCTTGAAACTCAAGGAAGCAGCTGTTAGACAGCGTGAAGCCCTAAAGAAGCTTACCAAGAATATAGCCACTGACTCATATATCAGTGTTAACTTGAGAGATGTCTATGCCCGGAGTATCATGGAGATGCTGCGACTGAAAGGCAGAGAAAGAGCAAGTACTAGGAGCAGCGGGGGAGATGATTTCTGGTTTTGA ->chimp -ATGCCTTCCAGCGGCAGAGCGCTGCTGGACTCGCCG---CTGGACAGCGGCTCCCTGACCTCCCTGGACTCTAGTGTCTTCTGCAGCGAGGGTGAAGGGGAGCCCTTGGCGCTCGGGGACTGCTTCACGGTCAACGTGGGCGGCAGCCGCTTCGTGCTCTCGCAGCAGGCGCTGTCCTGCTTCCCGCACACGCGCCTTGGCAAGCTGGCCGTGGTGGTGGCTTCCTACCGCCGCCCCGGGGCCCTGGCCGCCGTGCCCAGCCCTCTGGAGCTTTGCGACGATGCCAACCCCGTGGACAACGAGTACTTCTTCGACCGCAGCTCGCAGGCGTTCCGATATGTCCTGCACTACTACCGCACCGGCCGCCTGCATGTCATGGAGCAGCTGTGCGCGCTCTCCTTCCTGCAGGAGATCCAGTACTGGGGCATCGATGAGCTCAGCATCGATTCCTGCTGCAGGGACAG???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CCTGGAG???CCTGGATCTTCCACAGCTGCCCGTATCTTTGGTGTCATCTCCATTGTCTTCGTGGTGGTGTCCATCATTAACATGGCCCTGATGTCAGCTGAGTTAAGCTGGCTGGACCTGCAGCTGCTGGAAATCCTGGAGTATGTGTGCATTAGCTGGTTCACCGGGGAGTTTGTCCTCCGCTTCCTGTGTGTGCGGGACAGGTGTCGCTTCCTAAGAAAGGTGCCAAACATCATAGACCTCCTTGCCATCTTGCCCTTCTACATCACTCTTCTGGTAGAGAGCCTAAGTGGGAGCCAGACCACGCAGGAGCTGGAGAACGTGGGGCGCATTGTCCAGGTGTTGAGGCTGCTCAGGGCTCTGCGCATGCTAAAGCTGGGCAGACATTCCACAGGATTACGCTCCCTTGGGATGACAATCACCCAGTGTTACGAAGAAGTCGGCCTACTGCTCCTATTTCTATCCGTGGGAATCTCTATATTTTCAACTGTAGAATATTTTGCTGAGCAAAGCATTCCTGACACAACCTTCACAAGTGTCCCTTGTGCATGGTGGTGGGCCACCACCTCTATGACTACTGTGGGATATGGGGACATTAGACCAGACACCACCACAGGCAAAATCGTGGCCTTCATGTGTATATTATCGGGAATTCTTGTCTTGGCCTTGCCTATTGCTATTATTAACGATCGCTTCTCTGCTTGCTACTTCACCTTGAAACTCAAGGAAGCAGCTGTTAGACAGCGTGAAGCCCTAAAGAAGCTTACCAAGAATATAGCCACTGACTCATATATCAGTGTTAACTTGAGAGATGTCTATGCCCGGAGTATCATGGAGATGCTGCGACTGAAAGGCAGAGAAAGAGCAAGTACTAGGAGCAGCGGGGGAGATGATTTCTGGTTTTGA ->mouse -CTGTCACCCCGCAACCGGCCGCTACTGGACTCGTCGTCGCTGGACAGCGGTTCTCTGACCTCACTGGACTCCAGTGTTTTCTGTAGCGAGGGCGAAGGGGAACCCTTGGCTCTGGGGGACTGCTTTACAGTCAACGTGGGCGGTAGCCGCTTCGTGCTCTCGCAGCAAGCTCTGTCCTGCTTCCCGCACACGCGCCTGGGCAAACTGGCCGTAGTGGTGGCCTCCTACCGCCGCCTGGGTGCCCTGGCTGCCGCCCCCAGCCCCCTGGAGCTTTGCGATGATGCGAATCCGGTGGACAACGAGTACTTCTTTGATCGCAGCTCTCAGGCGTTCCGTTATGTCCTGCACTACTATCGCACTGGTCGCCTGCATGTCATGGAGCAGCTCTGTGCGCTCTCCTTTCTTCAGGAGATCCAGTACTGGGGCATAGATGAACTCAGCATTGACTCCTGCTGCAGGGACAGCCTTGTCCCACTGTCCGACAAAAGCTCTGGGATATTCTGGAGAAACCTGGATCTTCCACAGCAGCCCGGATCTTTGGAGTAATCTCCATCATTTTTGTGGCA----------------------------------------------------------------------------------------------------GTGTCCATCGTCAACATGGCCCTGATGTCAGCTGAGCTTAGCTGGCTCAACCTACAGCTGCTGGAGATCTTGGAGTATGTGTGCATCAGCTGGTTCACCGGGGAGTTCGTTCTGCGCTTCCTATGTGTGAAAGACAGGTGCCACTTCCTGAGGAAGGTTCCAAACATCATAGACCTCCTTGCCATCTTGCCCTTCTATATAACTCTTCTGGTGGAAAGCCTGAGCGGCAGCCACACCACACAAGAGCTGGAAAATGTGGGACGTCTGGTCCAGGTCTTGAGGCTCCTCAGAGCTCTGCGCATGCTGAAACTGGGAAGGCATTCTACAGGATTGCGCTCACTTGGGATGACAATCACTCAGTGCTATGAAGAAGTTGGCCTACTGCTCCTGTTTCTATCTGTGGGGATTTCTATATTTTCAACAATAGAATACTTTGCAGAGCAAAGCATTCCTGATACAACCTTCACAAGTGTTCCTTGTGCATGGTGGTGGGCCACAACATCCATGACTACAGTAGGATATGGGGACATTAGACCAGACACCACCACAGGCAAAATCGTGGCCTTCATGTGTATTCTGTCAGGAATCCTTGTCTTGGCCTTGCCTATTGCCATTATTAATGATCGATTCTCTGCTTGCTACTTCACCTTGAAACTCAAGGAAGCAGCTGTGAGACAGCGTGAAGCTCTCAAGAAACTTACCAAGAATATAGCCACTGACTCATATATTAGTGTTAACTTGAGGGATGTCTATGCCCGGAGCATAATGGAGATGCTTCGATTAAAGGGCAGGGAGAGAGCAAGTACTAGAAGCAGTGGTGGAGATGATTTCTGGTTTTAA - ->human -AGGAAAAGAAGCCCATCTGTGTCCAGAGATCAGAATAGAAGATACGACCAAAGGGAAGAAAGAGAGGAATATTCACAGTATGCTACTTCGGATACCGCAATGCCTAGATCTCCATCAGATTATGCTGATAGGCGATCTCAACATGAACCTCAGTTTTATGAAGACTCTGATCATTTAAGTTATAGGGACTCCAACAGGAGAAGTCATAGGCATTCCAAAGAATATATTGTAGATGATGAGGATGTGGAAAGCAGAGATGAATACGAAAGGCAAAGGAGAGAGGAAGAGTACCAGTCACGCTACCGAAGTGATCCGAATTTGGCCCGTTATCCAGTAAAGCCACAACCCTATGAAGAACAAATGCGGATCCATGCTGAAGTGTCCCGAGCACGGCATGAGAGAAGGCATAGTGATGTTTCTTTGGCAAATGCTGATCTGGAAGATTCCAGGATTTCTATGCTAAGGATGGATCGACCATCAAGGCAAAGATCTATATCAGAACGTAGAGCTGCCATGGAAAATCAGCGATCTTATTCAATGGAAAGAACTCGAGAGGCTCAGGGACCAAGTTCTTATGCACAAAGGACCACAAACCATAGTCCTCCTACCCCCAGGAGGAGTCCACTACCCATAGATAGACCAGACTTGAGGCGTACTGACTCACTACGGAAACAGCACCACTTAGATCCTAGCTCTGCTGTAAGAAAAACAAAACGGGAAAAAATGGAAACAATGTTAAGGAATGATTCTCTCAGTTCAGACCAGTCAGAGTCAGTGAGACCTCCACCACCAAAGCCTCATAAATCAAAGAAAGGCGGTAAAATGCGCCAGATTTCGTTGAGCAGTTCAGAGGAGGAATTGGCTTCCACGCCTGAATATACAAGTTGTGATGATGTTGAGATTGAAAGTGAGAGTGTAAGTGAAAAAGGGGACAGTCAAAAGGGAAAAAGAAAAACTAGTGAGCAGGCAGTTTTGTCGGACTCTAACACCAGGTCTGAGAGACAAAAGGAAATGATGTACTTTGGTGGCCACTCTTTGGAAGAGGATTTGGAATGGTCTGAACCTCAGATTAAGGACTCTGGGGTAGATACGTGTAGTAGCACAACCCTTAACGAGGAGCATAGCCATAGTGATAAGCACCCTGTAACCTGGCAACCATCTAAAGATGGAGATCGTTTAATTGGTCGCATTTTATTAAATAAGCGTCTAAAAGATGGAAGTGTACCTCGAGATTCAGGAGCAATGCTTGGCTTGAAGGTTGTAGGAGGAAAGATGACTGAATCAGGTCGGCTTTGTGCATTTATTACTAAAGTAAAAAAAGGAAGTTTAGCTGATACTGTAGGACATCTTAGACCAGGTGATGAAGTATTAGAATGGAATGGAAGACTACTGCAAGGAGCCACATTTGAGGAAGTGTACAACATCATTCTAGAATCCAAACCTGAACCACAAGTAGAACTTGTAGTTTCAAGGCCTATTGG???????????????????????????????????????????????GTTCTAGCTCCTTTGAATCTCAAAAAATGGATCGTCCTTCTATTTCTGTTACCTCTCCCATGAGTCCTGGAATGTTGAGGGATGTCCCA????????????????????????ATAAAACTATGGTTTGACAAGGTTGGTCACCAATTAATAGTTACAATTTTGGGAGCAAAAGATCTCCCTTCCAGGGAAGATGGGAGGCCAAGGAATCCTTATGTTAAAATTTACTTTCTTCCAGACAGAAG????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ATTTTAATTGAATTAGAAACAGCATTATTAGATGATGAGCCACATTGGTACAAACTTCAGACGCATGATGTCTCTTCATTGCCACTTCCCCACCCTTCTCCATATATGCCACGAAGACAGCTCCATGGAGAGAGCCCAACACGGAGGTTGCAAAGGTCAAAGAGAATAAGTGATAGTGAAGTCTCTGACTATGACTGTGATGATGGAATTGGTGTAGTATCAGATTATCGACATGATGGTCGAGATCTTCAAAGCTCAACATTATCAGTGCCAGAACAAGTAATGTCATCAAACCACTGTTCACCATCAGGGTCTCCTCATCGAGTAGATGTTATAGGAAGGACTAGATCATGGTCACCCAGTGTCCCTCCTCCACA???TCGGAATGTGGAACAGGGGCTTCGAGGGACCCGCACTATGACCGGACATTATAATACAATTAGCCGAATGGACAGACATCGTGTCATGGATGACCATTATTCTCCAGATAGAGACAGGGATTGTGAAGCAGCAGATAGACAGCCATATCACAGATCCAGATCAACAGAACAACGGCCTCTCCTTGAGCGGACCACCACCCGCTCCAGATCCACTGAACGTCCTGATACAAACCTCATGAGGTCGATGCCTTCATTAATGACTGGAAGATCTGCCCCTCCTTCACCTGCCTTATCGAGGTCTCATCCTCGTACTGGGTCTGTCCAGACAAGCCCATCAAGTACTCCAGTCGCAGGACGAAGGGGCCGACAGCTTCCACAGCTTCCACCAAAGGGAACGTTGGATAGAAAAGCAGGAGGTAAAAAACTAAGGAGCACTGTCCAAAGAAGTACAGAAACAGGCCTGGCCGTGGAAATGAGGAACTGGATGACTCGACAGGCAAGCCGAGAGTCTACAGATGGTAGCATGAACAGCTACAGCTCAGAAGGAAATCTGATTTTCCCTGGTGTTCGCTTGGCCTCTGATAGCCAGTTCAGTGATTTCCTGGATGGCCTTGGCCCTGCTCAGCTAGTGGGACGCCAGACTCTGGCAACACCTGCAATGGGTGACATTCAGGTAGGAATGATGGACAAAAAGGGACAGCTGGAGGTAGAAATCATCCGGGCCCGTGGCCTTGTTGTAAAACCAGGTTCCAAGACACTGCCAGCACCGTATGTAAAAGTGTATCTATTAGATAACGGAGTCTGCATAGCCAAAAAGAAAACAAAAGTGGCAAGAAAAACGCTGGAACCCCTTTACCAGCAGCTATTATCTTTCGAAGAGAGTCCACAAGGAAAAGTTTTACAGATCATCGTCTGGGGAGATTATGGCCGCATGGATCACAAATCTTTTATGGGAGTGGCCCAGATACTTTTAGATGAACTAGAGCTATCCAATATGGTGATCGGATGGTTCAAACTTTTCCCACCTTCCTCCCTAGTAGATCCAACCTTGGCCCCTCTGACAAGAAGAGCTTCCCAATCATCTCTGGAAAGTTCAACTGGACCTTCTTACTCTCGTTCATAG ->chimp -AGGAAAAGAAGCCCATCTGTGTCCAGAGATCAGAATAGAAGATACGACCAAAGGGAAGAAAGAGAGGAATATTCACAGTATGCTACTTCGGATACCGCAATGCCTAGATCTCCATCAGATTATGCTGATAGGCGATCTCAACATGAACCTCAGTTTTATGAAGACTCTGATCATTTAAGTTATAGGGACTCCAACAGGAGAAGTCATAGGCATTCCAAAGAATATATTGTAGATGATGAGGATGTGGAAAGCAGAGATGAATACGAAAGGCAAAGGAGAGAGGAAGAGTACCAGTCACGCTACCGAAGTGATCCGAATTTGGCCCGTTATCCAGTAAAGCCACAACCCTATGAAGAACAAATGCGGATCCATGCTGAAGTGTCCCGAGCACGGCATGAGAGAAGGC?TAGTGATGTTTCTTTGGCAAATGCTGATC??????????????????????????????????????????????????????????ATCAGAACGTAGA?CTGC???GGAAAATCA?C?A???TATTCA??GGAAAGA???????AGGCTCAGGGACCAA?TTCT???GCAC?AAG?AC???A?ACCATAGTCCTCCTACCCCCAGGAGGAGTCCACTACCCATAGATAGACCAGACTTGAGGCGTACTGACTCACTACGGAAACAGCACCACTTAGATCCTAGCTCTGCTGTAAGAAAAACAAAACGGGAAAAAATGGAAACGATGTTAAGGAATGATTCTCTCAGTTCAGACCAGTCAGAGTCAGTGAGACCTCCACCACCAAAGCCTCATAAATCAAAGAAAGGCGGTAAAATGC??????????????????????????????????????????????????????????????????????????????????????????????????????GGGACAGTCAAAAGGGAAAAAGAAAAAC?AGTGAGCAGGCAGTTTTGTCGGAC???AACACCAGG????AGAGACAAAAGGAAATGATGTACTTTG???GCCACTCTTTGGAAGAGGAT??GGAATGGTCTGAACCTCAGATTAAGGACTCTGGGGTAGATACGTGTAGTAGCACAACCC??AACGAGGAGCAT???????????????CACCCTGTAACCTGGCAACCATCTAAAGATGGAGATCGTTTAATTGGTCGCATTTTATTGAATAAGCGTCTAAAAGATGGAAGTGTACCTCGAGATTCAGGAGCAATGCTTGGCTTGAAGGTTGTAGGAGGAAAGATGACTGAATCAGGTCGGCTTTGTGCATTTATTACTAAAGTAAAAAAAGGAAGTTTAGCTGATACTGTAGGACATC?????????GTGATGAAGTATTAGAATGGAATGGAAGACTACTGCAAGGAGCCACATTTGAGGAAGTGTACAACATCATTCTAGAATCCAAACCTGAACCACAAGTAGAACTTGTAGTTTCAAGGCCTATTGG???????????????????????????????????????????????GTTCTAGCTCCTTTGAATCTCAAAAAATGGATCGTCCTTCTATTTCTGTTACCTCTCCCATGAGTCCTGGAATGTTGAGGGATGTCCCA????????????????????????ATAAAACTATGGTTTGACAAGGTTGGTCACCAATTAATAGTTACAATTTTGGGAGCAAAAGATCTCCCTTCCAGGGAAGATGGGAGGCCAAGGAATCCTTATGTTAAAATTTACTTTCTTCCAGACAGAAG????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ATTTTAATTGAATTAGAAACAGCATTATTAGATGATGAGCCACATTGGTACAAACTTCAGACGCATGATGTCTCTTCATTGCCACTTCCCCACCCTTCTCCATATATGCCACGAAGACAGCTCCATGGAGAGAGCCCAACACGGAGGTTGCAAA????????????????????????????CTCTGACTATGACTGTGATGATGGAAT?GGTGTA???????ATTATCGACATGATGGTCGAGATCTTCAAAGCTCAACATTATCAGTGCCAGAACAAGTAATGTCATCAAACCACTGTTCACCATCAGGGTCTCCTCATCGAGTAGA????ATAGGAAGGACTAGATCATGGTCACCCAGT?????????????????TCGGAATGTGGAACAGGGGCTTCGAGGGACCCG?ACTACGACCGGACATTATAATACAATTAGCCGAATGGATAGACATCGTGTCATGGATGACCATTATTCTCCAGATAGAGACAG????????????????????GACAGCCATATCA????TCCAGATCAACAGAACAACG???TCTTCTTG???GGACCACCACCCGCTCC???TCCACTGA?CGTCCTGATACAAACCTCA?????????????????????????????????????????????????????????????GTCTCATCCTCGTACTGGGTCTGTCCAGACAAGCCCATCAAGTACTCCAGTGGCAGGACGAAGGGGCCGACAGCTTCCACAGCTTCCACCAAAGGGAACGTTGGATAGAAAAGCAGGAGGTAAAAAACTAAGGAGCACTGTCCAAAGAAGTACAGAAACAGGCCTGGCCGTGGAAATGAGGAACTGGATGACTCGACAGGCAAGCCGAGAGTCTACAGATGGTAGCATGAACAGCTACAGCTCAGAAGGAAA????ATTTTCCCTGGTGTTCGCTTGGCCTCTGATAGCCAGTTCAGTGATTTCCTGGATGGCCTTGGCCCTGCTCAGCTAGTGGGACGCCAGACTCTGGCAACACCTGCAATGG??????????????????????????????????????????????????????????????????????????????????????????????????????CACCGTATGTAAAAGTGTATCTATTAGATAACGGAGTCTGCATAGCCAAAAAGAAAACAAAAGTGGCAAGAAAAACGCTGGAACCCCTTTACCAGCAGCTATTATCTTTCGAAGAGAGTCCACAAGGAAAAGTTTTACAG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->mouse -AGAAAACGAAGTCCATCAGTGTCCAGGGATCAAAATCGAAGATACGAGCAAAGTGAAGAAAGAGAGGACTACTCACAGTATGTTCCTTCAGATGGTACAATGCCAAGATCTCCTTCGGATTATGCTGATAGACGATCTCAGCGTGAGCCTCAATTTTATGAAGAACCTGGTCATTTAAATTACAGGGATTCTAACAGGAGAGGCCATAGACATTCCAAAGAGTATATTGTGGATGATGAAGATGTGGAGAGCAGAGATGAATATGAAAGACAAAGGAGAGAGGAGGAATACCAGGCACGCTACAGAAGTGATCCAAATCTGGCCCGGTATCCCGTAAAGCCACAACCCTACGAAGAACAAATGCGCATCCACGCTGAGGTGTCCAGGGCACGACATGAGAGAAGGCACAGTGATGTTTCTTTGGCAAACGCTGAACTAGAAGATTCCAGGATTTCTCTGCTAAGGATGGATAGACCATCAAGGCAAAGATCTGTATCTGAACGTAGAGCTGCAATGGAAAACCAACGATCGTATTCAATGGAAAGAACTCGAGAGGCTCAGGGACAAAGTTCTTATCCACAAAGGACCTCAAATCATAGTCCTCCCACCCCTCGGCGGAGCCCTATACCGCTTGATAGACCAGACATGAGGCGCGCTGACTCCCTACGGAAACAGCACCACTTAGATCCCAGCTCTGCTGTGAGGAAAACGAAGCGAGAAAAAATGGAAACCATGTTAAGGAATGATTCTTTGAGTTCAGACCAGTCCGAGTCAGTGAGGCCGCCCCCACCAAGGCCTCATAAATCCAAGAAAGGAGGTAAAATGCGCCAGGTTTCACTGAGCAGCTCGGAGGAGGAGCTGGCATCCACACCTGAGTATACAAGCTGTGATGATGTGGAGCTGGAAAGCGAGAGTGTGAGTGAGAAAGGGGACAGTCAAAAGGGAAAAAGAAAAACTAGTGAGCAGGGAGTTTTGTCGGATTCTAACACCAGGTCTGAGAGACAAAAGAAAAGGATGTACTATGGTGGCCACTCTTTGGAAGAGGATTTGGAATGGTCTGAGCCTCAGATTAAGGACTCTGGGGTAGATACCTGTAGTAGCACAACCCTTAACGAGGAGCATAGCCATAGTGATAAGCACCCTGTGACCTGGCAGCCATCCAAAGATGGAGATCGCCTAATTGGTCGTATTTTATTAAATAAGCGTTTAAAAGATGGGAGTGTACCTCGAGACTCAGGAGCAATGCTGGGCTTAAAGGTTGTAGGAGGAAAGATGACTGAATCAGGTCGACTTTGTGCATTTATTACCAAAGTAAAAAAAGGAAGTTTAGCTGATACTGTAGGACATCTTAGACCAGGTGATGAAGTCTTGGAATGGAATGGGAGGCTATTGCAAGGAGCCACATTTGAGGAAGTTTACAACATTATTCTAGAATCCAAACCTGAACCACAAGTTGAGCTTGTTGTTTCAAGGCCAATTGG???????????????????????????????????????????????GTTCTAGCTCATTTGAATCTCAAAAAATGGACCGTCCTTCTATATCCGTTACCTCACCCATGAGTCCTGG------------------------CATGCTGAGGGATGTCCCGATAAAACTATGGTTTGACAAGGTTGGTCACCAGTTGATAGTTACAATTTTGGGAGCAAAGGATCTCCCTTCCAGGGAAGATGGGAGGCCAAGGAATCCTTATGTTAAGATTTACTTCCTTCCAGATAGAAG????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ATTTTAATTGAATTGGAAACAGCTCTGCTAGATGATGAGCCGCACTGGTATAAGCTGCAGACCCATGATGTCTCCTCATTGCCACTCCCTCGCCCTTCCCCATATCTGCCCCGGAGGCAGCTCCATGGAGAGAGCCCAACGCGCAGGCTGCAAAGGTCGAAGAGAATAAGTGACAGTGAAGTGTCTGACTACGACTGCGAGGATGGCGTGGGAGTAGTGTCAGATTATCGACACAATGGCCGCGATCTTCAAAGCTCCACGTTGTCGGTGCCAGAACAAGTCATGTCATCAAATCATTGCTCACCATCAGGGTCTCCTCATCGAGTAGATGTTATAGGAAGGACAAGGTCATGGTCGCCTAGTGCCCCTCCTCC---TCATAGGAATGTGGAACAGGGGCACCGAGGGACACGTGCTA---CTGGCCATTACAACACAATTAGCCGAATGGATAGACACCGTGTCATGGATGACCACTACTCTTCAGATAGAGACAGGGATTGTGAAGCAGCAGATAGACAGCCATATCACAGATCCAGATCAACAGAACAACGGCCTCTCCTAGAGCGGACCACCACCCGCTCCAGATCCTCTGAACGTCCTGATACAAACCTCATGAGGTCGATGCCTTCATTAATGACTGGAAGATCTGCCCCTCCTTCACCTGCCTTATCGAGGTCTCACCCTCGTACCGGGTCTGTCCAGACAAGCCCATCAAGTACTCCGGGAACAGGACGAAGGGGCCGACAGCTTCCACAGCTTCCACCAAAGGGAACATTGGAGAGAAAAGGAGGAGGTAAAAAGCTACGGAGCACTGTTCAGAGAAGCACGGAGACCGGGCTAGCAGTGGAGATGAGGAACTGGATGACCCGCCAGGCCAGCCGGGAATCCACAGATGGCAGCATGAACAGCTATAGCTCGGAAGGAAATCTGATCTTCCCTGGGGTCCGCCTGGCCTCTGACAGCCAGTTCAGTGATTTCCTGGATGGCCTGGGCCCTGCTCAGCTAGTGGGACGCCAGACCCTGGCTACTCCTGCAATGGGTGACATTCAGGTGGGAATGATGGATAAAAAGGGACAGCTGGAGGTAGAAATCATCCGGGCGCGCGGCCTTGTGGTAAAACCAGGTTCCAAGACACTGCCAGCACCGTATGTCAAGGTGTATCTGTTAGACAACGGAGTCTGCATAGCCAAAAAGAAAACCAAGGTGGCGAGAAAGACCCTGGAGCCCCTGTACCAGCAGCTCTTGTCCTTCGAGGAGAGCCCCCAGGGGAGGGTGTTACAGATCATTGTCTGGGGAGATTATGGTCGTATGGATCACAAATCCTTTATGGGAGTGGCCCAGATACTCTTAGATGAACTGGAACTATCCAACATGGTGATTGGATGGTTCAAACTCTTCCCTCCTTCCTCCCTAGTAGATCCAACCTTGGCACCTCTGACAAGAAGAGCTTCCCAATCGTCTCTGGAAAGTTCTACCGGACCTTCTTACTCTCGTTCATAG - ->human -???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GGCACCTTCTCTCTGATTATTGAAGCTCTCCACACAGATTCTCCTGATGACCTCGCAACAGAAAACCCAGAAAGACTCATCAGCCGCCTGGCCACCCAGAGGCACCTGACGGTGGGCGAGGAGTGGTCCCAGGACCTGCACAGCAGCGGCCGCACGGACCTCAAGTACTCCTACCGCTTCGTGTGTGACGAACACTACTACGGAGAGGGCTGCTCCGTTTTCTGCCGTCCCCGGGACGATGCCTTCGGCCACTTCACCTGTGGGGAGCGTGGGGAGAAAGTGTGCAACCCTGGCTGGAAAGGGCCCTACTGCACAGAGCCGATCTGCCTGCCTGGATGTGATGAGCAGCATGGATTTTGTGACAAACCAGGGGAATGCAAGTGCAGAGTGGGCTGGCAGGGCCGGTACTGTGACGAGTGTATCCGCTATCCAGGCTGTCTCCATGGCACCTGCCAGCAGCCCTGGCAGTGCAACTGCCAGGAAGGCTGGGGGGGCCTTTTCTGCAACCAGGACCTGAACTACTGCACACACCATAAGCCCTGCAAGAATGGAGCCACCTGCACCAACACGGGCCAGGGGAGCTACACTTGCTCTTGCCGGCCTGGGTACACAGGTGCCACCTGCGAGCTGGGGATTGACGAGTGTGACCCCAGCCCTTGTAAGAACGGAGGGAGCTGCACGGATCTCGAGAACAGCTACTCCTGTACCTGCCCACCCGGCTTCTACGGCAAAATCTGTGAATTGAGTGCCATGACCTGTGCGGACGGCCCTTGCTTTAACGGGGGTCGGTGCTCAGACAGCCCCGATGGAGGGTACAGCTGCCGCTGCCCCGTGGGCTACTCCGGCTTCAACTGTGAGAAGAAAATTGACTACTGCAGCTCTTCACCCTGTTCTAATGGTGCCAAGTGTGTGGACCTCGGTGATGCCTACCTGTGCCGCTGCCAGGCCGGCTTCTCGGGGAGGCACTGTGACGACAACGTGGACGACTGCGCCTCCTCCCCGTGCGCCAACGGGGGCACCTGCCGGGATGGCGTGAACGACTTCTCCTGCACCTGCCCGCCTGGCTACACGGGCAGGAACTGCAGTGCCCCCGTCAGCAGGTGCGAGCACGCACCCTGCCACAATGGGGCCACCTGCCACGAGAGGGGCCACCGCTATGTGTGCGAGTGTGCCCGAGGCTACGGGGGTCCCAACTGCCAGTTCCTGCTCCCCGAGCTGCCCCCGGGCCCAGCGGTGGTGGACCTCACTGAGAAGC---TAGAGGGCCAGGGCGGGCCATTCCCCTGGGTGGCCGTGTGCGCCGGGGTCATCCTTGTCCTCATGCTGCTGCTGGGCTGTGCCGCTGTGGTGGTCTGCGTCCGGCTGAGGCTGCAGAAGCACCGGCCCCCAGCCGACCCCTGCCGGGGGGAGACGGAGACCATGAACAACCTGGCCAACTGCCAGCGTGAGAAGGACATCTCAGTCAGCATCATCGGGGCCACGCAGATCAAGAACACCAACAAGAAGGCGGACTTCCACGGGGACCACAGCGCCGACAAGAATGGCTTCAAGGCCCGCTACCCAGCGGTGGACTATAACCTCGTGCAGGACCTCAAGGGTGACGACACCGCCGTCAGGGACGCGCACAGCAAGCGTGACACCAAGTGCCAGCCCCAGGGCTCCTCAGGGGAGGAGAAGGGGACCCCGACCACACTCAGGGGTGGAGAAGCATCTGAAAGAAAAAGGCCGGACTCGGGCTGTTCAACTTCAAAAGACACCAAGTACCAGTCGGTGTACGTCATATCCGAGGAGAAGGATGAGTGCGTCATAGCAACTGAG?????? ->chimp -???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GGCACCTTCTCTCTGATTATTGAAGCTCTCCACACAGATTCTCCTGATGACCTCGCAACAGAAAACCCAGAAAGACTCATCAGCCGCCTGGCCACCCAGAGGCA?CTGACGGTGGGCGAGGAGTGGTCCCAGGACCTGCACAGCAGCGGCCGCACGGACCTCAAGTACTCCTACCGCTTCGTGTGTGACGAACACTACTACGGAGAGGGCTGCTCCGTTTTCTGCCGTCCCCGGGACGATGCCTTCGGCCACTTCACCTGTGGGGAGCGTGGGGAGAAAGTGTGCAACCCTGGCTGGAAAGGGCCCTACTGCACAGAGCCGATCTGCCTGCCTGGATGTGATGAGCAGCATGGATTTTGTGACAAACCAGGGGAATGCAA???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????ACCTGAACTACTGCACACACCATAAGCCCTGCA????TGGGGCCACCTGCACCAACAC??G??A???GAGCTACACTTGCTCTTGCCGGCCTGGGTACAC??????????????????????????????????????????????????????????????????????GATCTCGAGAACAGCTACTCCTGTACCTGCCCACCCGGCTTCTACGGCAAAATCTGTGAATTGAGTGCCATGACCTGTGCGGACGGCCCTTGCTTTAACGGGGGCCGGTGCTCAGACAGCCCCGATGGAGGGTACAGCTGCCGCTGCCCCGTGGGCTACTCCGGCTTCAACTGTGAGAAGAAAATTGACTACTGCAGCTCTTCACCCTGTTCTAATGGTGCCAAGTGTGTGGA??TCGGTGATGCCTACCTGTGCCGCTGCCAGGCCGG???????GGGAGGCACTGTGACGACAACGTGGATG???GCGCCTCCTCCCCGTGCGCCAACGGGGGCACCTGCCGGGATGGCGTGAACGACT?????TGCACCTGCCCGCCCGGCTACACGGGCAGGAACTGCAGTGCCCCCGTCAGCAGGTGCGAGCACGCACCCTGCCACAATGGGGCCACCTGCCACGAGAGGGGCCACCGCTATGTGTGCGAGTGTGCCCGAGGCTACGGGGGTCCCAACTGCCAGTTCCTGCTCCCCGAGCTGCCCCCGGGCCCAGCGGTGGTGGACCTCACTGAGAAGC---TAGAGGGCCAGGGCGGGCCATTCCCCTGGGTGGCCGTGTGCGCCGGGGTCATCCTTGTCCTCATGCTGCTGCTGGGCTGTGCCGCTGTGGTGGTCTGCGTCCGGCTGAGGCTGCAGAAGCACCGGCCCCCAGCCGACCCCTGCCGGGGGGAGACGGAGACCATGAACAACCTGGCCAACTGCCAGCGTGAGAAGGACATCTCAGTCAGCATCATCGGGGCCACGCAGATCAAGAACACCAACAAGAAGGCGGACTTCCACGGGGACCACAGCGCCGACAAGAATGGCTTCAAGGCCCGCTACCCGGCGGTGGACTATAACCTCGTGCAGGACCTCAAGGGTGACGACACCGCCGTCAGGGACGCGCACAGCAAGCGTGACACCAAGTGCCAGCCCCAGGGCTCCTCAGGGGAGGAGAAGGGGACCCCAACCACACTCAGGGGTGGAGAAGCATCTGAAAGAAAAAGGCCGGACTCGGGCTGTTCGACTTCAAAAGACACCAAGTACCAGTCGGTGTACGTCATATCCGAGGAGAAGGATGAGTGCGTCATAGCAACTGAG?????? ->mouse -???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GGTACCTTCTCTCTGATCATTGAAGCCCTCCATACAGACTCTCCCGATGACCTCGCAACAGAAAACCCAGAAAGACTCATCAGCCGCCTGACCACACAGAGGCACCTCACTGTGGGAGAAGAATGGTCTCAGGACCTTCACAGTAGCGGCCGCACAGACCTCCGGTACTCTTACCGGTTTGTGTGTGACGAGCACTACTACGGAGAAGGTTGCTCTGTGTTCTGCCGACCTCGGGATGACGCCTTTGGCCACTTCACCTGCGGGGACAGAGGGGAGAAGATGTGCGACCCTGGCTGGAAAGGCCAGTACTGCACTGACCCAATCTGTCTGCCAGGGTGTGATGACCAACATGGATACTGTGACAAACCAGGGGAGTGCAAGTGCAGAGTTGGCTGGCAGGGCCGCTACTGCGATGAGTGCATCCGATACCCAGGTTGTCTCCATGGCACCTGCCAGCAACCCTGGCAGTGTAACTGCCAGGAAGGCTGGGGGGGCCTTTTCTGCAACCAAGACCTGAACTACTGTACTCACCATAAGCCGTGCAGGAATGGAGCCACCTGCACCAACACGGGCCAGGGGAGCTACACATGTTCCTGCCGACCTGGGTATACAGGTGCCAACTGTGAGCTGGAAGTAGATGAGTGTGCTCCTAGCCCCTGCAAGAACGGAGCGAGCTGCACGGACCTTGAGGACAGCTTCTCTTGCACCTGCCCTCCCGGCTTCTATGGCAAGGTCTGTGAGCTGAGCGCCATGACCTGTGCAGATGGCCCTTGCTTCAATGGAGGACGATGTTCAGATAACCCTGACGGAGGCTACACCTGCCATTGCCCCTTGGGCTTCTCTGGCTTCAACTGTGAGAAGAAGATGGATCTCTGCGGCTCTTCCCCTTGTTCTAACGGTGCCAAGTGTGTGGACCTCGGCAACTCTTACCTGTGCCGGTGCCAGGCTGGCTTCTCCGGGAGGTACTGCGAGGACAATGTGGATGACTGTGCCTCCTCCCCGTGTGCAAATGGGGGCACCTGCCGGGACAGTGTGAACGACTTCTCCTGTACCTGCCCACCTGGCTACACGGGCAAGAACTGCAGCGCCCCTGTCAGCAGGTGTGAGCATGCACCCTGCCATAATGGGGCCACCTGCCACCAGAGGGGCCAGCGCTACATGTGTGAGTGCGCCCAGGGCTATGGCGGCCCCAACTGCCAGTTTCTGCTCCCTGAGCCACCACCAGGGCCCATGGTGGTGGACCTCAGTGAGAGGCATATGGAGAGCCAGGGCGGGCCCTTCCCCTGGGTGGCCGTGTGTGCCGGGGTGGTGCTTGTCCTCCTGCTGCTGCTGGGCTGTGCTGCTGTGGTGGTCTGCGTCCGGCTGAAGCTACAGAAACACCAGCCTCCACCTGAACCCTGTGGGGGAGAGACAGAAACCATGAACAACCTAGCCAATTGCCAGCGCGAGAAGGACGTTTCTGTTAGCATCATTGGGGCTACCCAGATCAAGAACACCAACAAGAAGGCGGACTTTCACGGGGACCATGGAGCCGAGAAGAGCAGCTTTAAGGTCCGATACCCCACTGTGGACTATAACCTCGTTCGAGACCTCAAGGGAGATGAAGCCACGGTCAGGGATACACACAGCAAACGTGACACCAAGTGCCAGTCACAGAGCTCTGCAGGAGAAGAGAAGATCGCCCCAAC---ACTTAGGGGTGGGGAGATTCCTGACAGAAAAAGGCCAGAGTCTGTCTACTCTACTTCAAAGGACACCAAGTACCAGTCGGTGTATGTTCTGTCTGCAGAAAAGGATGAGTGTGTTATAGCGACTGAG?????? - ->human -ATGGTCTGGAGGCTGGTCCTGCTGGCTCTGTGGGTGTGGCCCAGCACGCAAGCTGGTCACCAGGACAAAGACACGACCTTCGACCTTTTCAGTATCAGCAACATCAACCGCAAGACCATTGGCGCCAAGCAGTTCCGCGGGCCCGACCCCGGCGTGCCGGCTTACCGCTTCGTGCGCTTTGACTACATCCCACCGGTGAACGCAGATGACCTCAGCAAGATCACCAAGATCATGCGGCAGAAGGAGGGCTTCTTCCTCACGGCCCAGCTCAAGCAGGACGGCAAGTCCAGGGGCACGCTGTTGGCTCTGGAGGGCCCCGGTCTCTCCCAGAGGCAGTTCGAGATCGTCTCCAACGGCCCCGCGGACACGCTGGATCTCACCTACTGGATTGACGGCACCCGGCATGTGGTCTCCCTGGAGGACGTCGGCCTGGCTGACTCGCAGTGGAAGAACGTCACCGTGCAGGTGGCTGGCGAGACCTACAGCTTGCACGTGGGCTGCGACCTCATAGACAGCTTCGCTCTGGACGAGCCCTTCTACGAGCACCTGCAGGCGGAAAAGAGCCGGATGTACGTGGCCAAAGGCTCTGCCAGAGAGAGTCACTTCAGGGGTTTGCTTCAGAACGTCCACCTAGTGTTTGAAAACTCTGTGGAAGATATTCTAAGCAAGAAGGGTTGCCAGCAAGGCCAGGGAGCTGAGATCAACGCCATCAGTGAGAACACAGAGACGCTGCGCCTGGGTCCGCATGTCACCACCGAGTACGTGGGCCCCAGCTCGGAGAGGAGGCCCGAGGTGTGCGAACGCTCGTGCGAGGAGCTGGGAAACATGGTCCAGGAGCTCTCGGGGCTCCACGTCCTCGTGAACCAGCTCAGCGAGAACCTCAAGAGAGTGTCGAATGATAACCAGTTTCTCTGGGAGCTCATTGGTGGCCCTCCTAAGACAAGGAACATGTCAGCTTGCTGGCAGGATGGCCGGTTCTTTGCGGAAAATGAAACGTGGGTGGTGGACAGCTGCACCACGTGTACCTGCAAGAAATTTAAAACCATTTGCCACCAAATCACCTGCCCGCCTGCAACCTGCGCCAGTCCATCCTTTGTGGAAGGCGAATGCTGCCCTTCCTGCCTCCACTCGGTGGACGGTGAGGAGGGCTGGTCTCCGTGGGCAGAGTGGACCCAGTGCTCCGTGACGTGTGGCTCTGGGACCCAGCAGAGAGGCCGGTCCTGTGACGTCACCAGCAACACCTGCTTGGGGCCCTCCATCCAGACACGGGCTTGCAGTCTGAGCAAGTGTGACACCCGCATCCGGCAGGACGGCGGCTGGAGCCACTGGTCACCTTGGTCTTCATGCTCTGTGACCTGTGGAGTTGGCAATATCACACGCATCCGTCTCTGCAACTCCCCAGTGCCCCAGATGGGGGGCAAGAATTGCAAAGGGAGTGGCCGGGAGACCAAAGCCTGCCAGGGCGCCCCATGCCCAATCGATGGCCGCTGGAGCCCCTGGTCCCCGTGGTCGGCCTGCACTGTCACCTGTGCCGGTGGGATCCGGGAGCGCACCCGGGTCTGCAACAGCCCTGAGCCTCAGTACGGAGGGAAGGCCTGCGTGGGGGATGTGCAGGAGCGTCAGATGTGCAACAAGAGGAGCTGCCCCGTGGATGGCTGTTTATCCAACCCCTGCTTCCCGGGAGCCCAGTGCAGCAGCTTCCCCGATGGGTCCTGGTCATGCGGCTCCTGCCCTGTGGGCTTCTTGGGCAATGGCACCCACTGTGAGGACCTGGACGAGTGTGCCCTGGTCCCCGACATCTGCTTCTCCACCAGCAAGGTGCCTCGCTGTGTCAACACTCAGCCTGGCTTCCACTGCCTGCCCTGCCCGCCCCGATACAGAGGGAACCAGCCCGTCGGGGTCGGCCTGGAAGCAGCCAAGACGGAAAAGCAAGTGTGTGAGCCCGAAAACCCATGCAAGGACAAGACACACAACTGCCACAAGCACGCGGAGTGCATCTACCTGGGCCACTTCAGCGACCCCATGTACAAGTGCGAGTGCCAGACAGGCTACGCGGGCGACGGGCTCATCTGCGGGGAGGACTCGGACCTGGACGGCTGGCCCAACCTCAATCTGGTCTGCGCCACCAACGCCACCTACCACTGCATCAAGGATAACTGCCCCCATCTGCCAAATTCTGGGCAGGAAGACTTTGACAAGGACGGGATTGGCGATGCCTGTGATGATGACGATGACAATGACGGTGTGACCGATGAGAAGGACAACTGCCAGCTCCTCTTCAATCCCCGCCAGGCTGACTATGACAAGGATGAGGTTGGGGACCGCTGTGACAACTGCCCTTACGTGCACAACCCTGCCCAGATCGACACAGACAACAATGGAGAGGGTGACGCCTGCTCCGTGGACATTGATGGGGACGATGTCTTCAATGAACGAGACAATTGTCCCTACGTCTACAACACTGACCAGAGGGACACGGATGGTGACGGTGTGGGGGATCACTGTGACAACTGCCCCCTGGTGCACAACCCTGACCAGACCGACGTGGACAATGACCTTGTTGGGGACCAGTGTGACAACAACGAGGACATAGATGACGACGGCCACCAGAACAACCAGGACAACTGCCCCTACATCTCCAACGCCAACCAGGCTGACCATGACAGAGACGGCCAGGGCGACGCCTGTGACCCTGATGATGACAACGATGGCGTCCCCGATGACAGGGACAACTGCCGGCTTGTGTTCAACCCAGACCAGGAGGACTTGGACGGTGATGGACGGGGTGATATTTGTAAAGATGATTTTGACAATGACAACATCCCAGATATTGATGATGTGTGTCCTGAAAACAATGCCATCAGTGAGACAGACTTCAGGAACTTCCAGATGGTCCCCTTGGATCCCAAAGGGACCACCCAAATTGATCCCAACTGGGTCATTCGCCATCAAGGCAAGGAGCTGGTTCAGACAGCCAACTCGGACCCCGGCATCGCTGTAGGTTTTGACGAGTTTGGGTCTGTGGACTTCAGTGGCACATTCTACGTAAACACTGACCGGGACGACGACTATGCCGGCTTCGTCTTTGGTTACCAGTCAAGCAGCCGCTTCTATGTGGTGATGTGGAAGCAGGTGACGCAGACCTACTGGGAGGACCAGCCCACGCGGGCCTATGGCTACTCCGGCGTGTCCCTCAAGGTGGTGAACTCCACCACGGGGACGGGCGAGCACCTGAGGAACGCGCTGTGGCACACGGGGAACACGCCGGGGCAGGTGCGAACCTTATGGCACGACCCCAGGAACATTGGCTGGAAGGACTACACGGCCTATAGGTGGCACCTGACTCACAGGCCCAAGACTGGCTACATCAG???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->chimp -ATGGTCTGGAGGCTGGTCCTGCTGGCTCTGTGGGTGTGGCCCAGCACGCAAG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GATCACCAAGATCATGCGGCAGAAGGAGGGCTTCTTCCTCACGGCCCAGCTCAAGCAGGACGGCAAGTCCAGGGGCACGCTGTTGGCTCTGGAGGGCCCCGGTCTCTCCCAGAGGCAGTTCGAGATCGTCTCCAATGGCCCCGCGGACACGCTGGATCTCACCTACTGGATTGACGGCACCCGGCACGTGGTCTCCCTGGAGGACGTCGGCCTGGCTGACTCGCAGTGGAAGAACGTCACCGTGCAGGTGGCTGGCGAGACCTACAGCTTGCACGTGGGCTGCGACCTCATAGACAGCTTCGCTCTGGACGAGCCCTTCTACGAGCACCTGCAGGCGGAAAAGAGCCGGATGTACGTGGCCAAAGGCTCTGCCAGAGAGAGTCACTTCAGGGGTTTGCTTCAGAACGTCCACCTAGTGTTTGAAAACTCTCTGGAAGACATTCTAAGCAAGAAGGGTTGCCAGCAAGGCC???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????TCGAATGATAACCAGTTTCTCTGGGAGCTCATCGGTGGCCCTCCTAAGACAAGGAACATGTCAGCTTGCTGGCAGGATGGCCGGTTCTTTGCGGAAAATGAAACGTGGGTGGTGGACAGCTGCACCTCGTGTACCTGCAAGAAATTTAAAACCATTTGCCACCAAATCACCTGCCCGCCTGCAACCTGCGCCAGTCCGTCCTTTGTGGAAG???AATGCT???CTTCCTGCCTCCACTCGGTGGACGGTGAGGAGGGCTGGTCTCCGTGGGCAGAGTGGACCCAGTGCTCTGTGACGTGTGGCTCTGGGACCCAGCAGAGAGGCCGGTCCTGTGACGTCACCAGCAACACCTGCTTGGGGCCCTCCATCCAGACACGGGCTTGCAGTCTGAGCAAGTGTGACACCCGCATCCGGCAGGACGGCGG???GAGCCAC??GTCACCTTGGTCTTCATGCT???TGAC?????GAG??GGCA??ATCACACGCATCCGT?TCTGC?????CCCAGTGCCCCAG???GGGGGCAAGAA???CAAAGGGAGTGGCCGGGAGACCAAAGCCTGCCAGGGCGCCCCATGCCCAATCGATGGCCGCTGGAGCCCCTGGTCCCCGTGGTCGGCCTGCACTGTCACCTGTGCCGGTGGGATCCGGGAGCGCACCCGGGTCTGCAACAGCCCTGAGCCTCAGTACGGAGGGAAGGCCTGCGTGGGGGATGTGCAGGAGCGTCAGATGTGCAACAAGAGGAGCTGCCCCGTGG?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GTGTGTGAGCCCGAAAACCCATGCAAGGACAAGACACACAACTGCCACAAGCACGCGGAGTGCATCTACCTGGGCCACTTCAGCGACCCCATGTACAAGTGCGAGTGCCAGACAGGCTACGCGGGCGACGGGCTCATCTGCGGGGAGGACTCGGACCTGGACGGCTGGCCCAACCTCAATCTGGTCTGCGCCACCAACGCCACCTACCACTGCATCAAGGATAACTGCCCCCATCTGCCAAATTCTGGGCAGGAAGACTTTGACAAGGACGGGATTGGCGATGCCTGTGATGATGACGATGACAATGACGGTGTGACCGATGAGAAG???????????????????????????????????TGACTATGACAAGGATG???TTGGGGACCGCT???ACAACTGCCCTTAC????????????????????????????????????????????????????????????????????????????ATGTCTTCAATGAACGAGACAATTGTCCCTACGTCTACAACACTGACCAGAGGGACACGGATGGTGACGGTGTGGGGGATC??????????????????????????????????????ACCGACGTGGACAATGACCTTGTTGGGGACCAGTGTGACAACAACGAGGACATAGATGATGACGGCCACCAGAACAACCAGGACAACTGCCCCTACATCTCCAACGCCAACCAGGCTGACCATGACAGAGACGGCCAGGGCGACGCCTGTGACCCCGATGATGACAACGATGGCGTCCCCGATGACAGGGACAACTGCCGGCTTGTGTTCAACCCAGACCAGGAGGACTTGGACGGTGATGGACGGGGTGATATTTGTAAAGATGATTTTGACAATGAC??CATCCC???TATTGATGATGTGTGTCCTGAAAACAATGCCATCAGTGAGACAGACTTCAGGAACTTCCAGATGGTCCCCTTGGATCCCAAAGGGACCACCCAAATTGATCCCAACTGGGTCATTCGCCATCAAGGCAAGGAGCTGGTTCAGACAGCCAACTCGGACCCTGGCATCGCTGTAGGTTTTGACGAGTTTGGGTCTGTGGACTTCAGTGGCACATTCTACGTAAACACTGACCGGGACGACGACTATGCCGGCTTCGTCTTTGGTTACCAGTCAAGCAGCCGCTTCTATGTGGTGATGTGGAAGCAGGTGACGCAGACCTACTGGGAGGACCAGCCCACGCGGGCCTATGGCTACTCCGGCGTGTCCCTCAAGGTGGTGAACTCCACCACAGGGACGGGCGAGCACCTGAGGAACGCGCTGTGGCACACGGGGAACACGCCGGGGCAG?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? ->mouse -ATGCTCTGGGCACTGGCCCTGCTGGCTCTGGGCATAGGGCCAAGAGCTTCTGCTGGTGACCACGTCAAGGACACTTCATTTGACCTTTTCAGCATCAGCAACATTAACCGGAAGACCATCGGTGCCAAGCAGTTCCGAGGGCCTGACCCCGGGGTGCCCGCCTACCGTTTTGTACGGTTTGACTACATCCCCCCAGTGAACACAGATGATCTCAACAGGATTGTCAAGCTTGCAAGGAGAAAGGAGGGCTTCTTCCTCACAGCCCAACTGAAGCAGGACCGCAAGTCTCGGGGAACGCTCCTGGTGTTGGAAGGCCCCGGCACCTCCCAGAGGCAGTTTGAGATTGTGTCCAATGGCCCAGGGGACACTTTGGACCTCAACTACTGGGTAGAAGGCAATCAGCATACCAACTTCCTGGAGGATGTGGGCCTGGCTGACTCCCAGTGGAAGAATGTGACTGTGCAGGTGGCCAGTGACACCTATAGCCTGTATGTGGGCTGCGATCTTATCGACAGTGTCACCCTGGAAGAACCATTCTATGAGCAGCTAGAAGTAGACAGGAGCAGGATGTACGTGGCCAAAGGTGCATCTCGAGAGAGTCACTTCAGGGGCTTGCTGCAGAATGTCCATCTCGTATTTGCAGATTCTGTGGAAGATATCTTAAGCAAGAAAGGCTGTCAACACAGCCAGGGAGCTGAAGTCAACACCATCAGTGAACATACAGAGACTCTCCATCTGAGCCCTCACATCACCACAGATCTCGTGGTCCAGGGTGTGGAGAAGGCACAGGAGGTGTGTACGCACTCCTGCGAGGAGTTGAGCAACATGATGAATGAGCTCTCTGGACTGCACGTCATGGTGAACCAGCTGAGCAAGAACCTGGAGAGAGTGTCTAGTGATAACCAGTTCCTTTTGGAGCTCATTGGGGGCCCTCTGAAGACAAGAAACATGTCAGCCTGTGTGCAGGAGGGCCGAATCTTTGCAGAAAATGAAACCTGGGTTGTGGATAGTTGTACCACATGCACCTGCAAGAAATTTAAAACAGTCTGCCATCAGATCACCTGCTCACCTGCAACTTGTGCCAACCCATCTTTTGTGGAAGGCGAGTGCTGTCCATCCTGTTCACACTCTGCAGACAGTGATGAGGGCTGGTCTCCGTGGGCAGAGTGGACCGAGTGTTCTGTCACCTGTGGCTCTGGGACCCAGCAGAGAGGCCGGTCTTGTGATGTCACCAGCAACACCTGCCTGGGCCCCTCCATTCAGACAAGGACATGCAGCCTGGGCAAATGTGATACGAGAATCCGTCAGAATGGAGGCTGGAGTCACTGGTCACCCTGGTCTTCATGCTCCGTGACTTGTGGAGTTGGCAATGTCACCCGCATACGTCTCTGCAACTCACCAGTGCCCCAGATGGGTGGCAAGAACTGCAAGGGCAGCGGCCGGGAAACCAAACCCTGTCAGCGTGATCCGTGCCCAATTGATGGCCGCTGGAGCCCCTGGTCCCCTTGGTCAGCCTGCACAGTTACCTGTGCTGGAGGGATCCGTGAGCGCTCACGTGTTTGCAACAGCCCTGAGCCCCAGTATGGAGGGAAGGACTGTGTCGGGGATGTGACAGAACACCAAATGTGCAACAAGAGAAGCTGCCCTATTGATGGGTGCTTATCCAACCCGTGTTTTCCTGGAGCCAAGTGCAACAGCTTCCCTGATGGGTCCTGGTCCTGTGGCTCCTGCCCAGTGGGCTTTCTGGGCAATGGTACCCACTGTGAGGACCTGGATGAGTGTGCTGTGGTCACAGATATTTGCTTCTCAACTAACAAAGCTCCCCGCTGTGTCAACACCAACCCGGGCTTCCACTGCCTGCCTTGTCCACCACGCTACAAGGGGAACCAACCCTTCGGTGTTGGCCTGGAGGATGCTAGGACAGAAAAACAAGTGTGTGAGCCAGAGAATCCATGTAAGGACAAGACTCACAGCTGCCACAAGAATGCAGAGTGCATCTACCTGGGCCACTTTAGTGACCCCATGTACAAGTGTGAGTGCCAGATTGGCTACGCAGGTGATGGGCTCATCTGCGGGGAGGACTCAGACCTGGATGGCTGGCCCAACAACAACCTGGTGTGTGCTACTAATGCCACCTACCACTGCATCAAGGACAACTGCCCCAAACTGCCAAATTCCGGGCAGGAGGATTTTGATAAGGATGGAATCGGAGATGCTTGTGACGAGGACGATGACAATGACGGTGTGAGCGATGAGAAGGACAATTGCCAGCTTCTCTTCAATCCCCGTCAATTAGACTATGACAAGGATGAGGTTGGAGACCGCTGTGACAACTGCCCCTATGTGCACAACCCAGCACAGATCGACACAGACAACAATGGCGAGGGGGATGCCTGCTCTGTGGACATTGACGGAGACGATGTTTTCAATGAGCGAGACAATTGTCCATATGTCTACAACACTGACCAGAGAGATACGGATGGTGATGGCGTGGGTGACCACTGTGACAATTGTCCTCTGATGCACAACCCAGATCAGATCGATCAGGACAATGATCTCGTTGGAGACCAGTGTGACAACAATGAGGACATAGATGATGACGGCCACCAGAACAACCAAGACAACTGCCCATACATCTCCAACTCCAACCAGGCTGACCATGACAACGACGGCAAGGGCGATGCCTGCGACTCTGATGATGACAATGATGGTGTTCCAGATGACAGGGACAACTGTCGGCTTGTGTTCAACCCAGACCAGGAAGACTCGGACGGTGACGGCCGAGGTGACATTTGTAAAGATGACTTTGACAATGATAATGTCCCAGATATTGATGATGTGTGCCCTGAGAACAATGCCATCACTGAGACAGACTTCAGAAACTTCCAGATGGTCCCTCTGGATCCCAAGGGGACCACACAAATTGATCCCAACTGGGTAATTCGTCACCAAGGCAAAGAGCTGGTGCAGACAGCAAACTCAGACCCTGGCATCGCTGTAGGTTTCGACGAGTTTGGGTCTGTGGACTTCAGTGGCACTTTCTATGTCAACACTGACCGGGATGATGACTACGCTGGCTTTGTCTTTGGCTATCAGTCAAGCAGCCGCTTCTATGTGGTGATGTGGAAGCAGGTGACCCAGACCTACTGGGAAGACAAGCCCAGTCGGGCTTACGGCTACTCTGGTGTGTCACTCAAAGTGGTAAACTCCACGACTGGTACTGGCGAGCACCTGAGGAATGCCCTGTGGCACACGGGAAACACAGAAGGCCAGGTCCGGACTCTATGGCATGACCCCAAAAACATTGGCTGGAAAGACTACACTGCCTACAGGTGGCACCTGATTCACAGGCCTAAGACAGGCTACATGAG???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? - ->human -????????????????TACAAGATATGGAGCAATTTTACGAACTATGGCTCAAGAGTCAAAAAAATGAAAAAAGTGAAGACATAGCCAGTCAGTCAAACAAGGAAAATGGAAAACAAATTCACATGCCAACAGATTATGCTGAAGTTACAGTGGACTTTCACTGCTGGATGTGTGGGAAAAACTGCAACAGTGAGAAGCAGTGGCAGGGCCACATCTCCTCCGAGAAGCACAAAGAGAAGGTTTTCCACACCGAGGACGACCAGTACTGCTGGCAGCACCGCTTCCCAACAGGCTATTTCAGTATTTGTGATAGGTATATGAATGGCACCTGCCCAGAAGGAAACAGCTGTAAATTTGCACATGGAAATGCCGAACTTCATGAATGGGAAGAAAGAAGAGATGCCCTAAAGATGAAGCTCAACAAAGCACGAAAAGATCACTTAATTGGCCCAAATGATAATGACTTTGGAAAATATAGTTTTTTGTTTAAAGATTTAAACTAA ->chimp -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GTGGACTTTCACTGCTGGATGTGTGGGAAAAACTGCAACAGTGAGAAGCAGTGGCAGGGCCACATCTCCTCCGAGAAGCACAAAGAGAAGGTTTTCCACACCGAGGACGACCAGTACTGCTGGCAGCACCGCTTCCCAACAGGCTATTTCAGTATTTGTGATAGGTATATGAATGGCACCTGCCCAGAAGGAAACAGCTGTAAATTTGCACATGGAAATGCCGAACTTCATGAATGGGAAGAAAGAAGAGATGCCCTAAAGATGAAGCTCAACAAAGCACGAAAAGATCACTTAATTGGCCCAAATGATAATGACTTTGGAAAATATAGTTTTTTGTTTAAAGATTTAAACTAA ->mouse -????????????????TACATGATATAGAGCAATTTTATGAACTCTGGCTGAAGAACCAAAAAACTGAAAAAAGTGATGAGACAGCCAGTCACTGTAGCAAAGAAAACGGGAAGCAGATCCATATGCCAACAGACTATGCTGAAGTCACTGTGGACTTCCACTGCTGGATGTGTGGGAAGAACTGTAACAGTGAGAAGCAATGGCAAGACCACATCTCCTCTGAGAAGCACAAGGAGAAGGTTTTCCACACTGAGGATGACCAGTACTGCTGGCAGCACCGCTTCCCCACTGGGTACTTCAGTATTTGTGAGAGGTATATAAATGGCTCCTGCACAGAAGGAAGCAGCTGTAAATTTGCACATGGAAATGCTGAACTTCATGAATGGGAAGAAAGAAGAAAGGCCCTACAGATGAAATTCAAGAAAGCACGGAAAGATCACTTAATTGCCCCAAATGATAATGACTTTGGAAAATATAGTTTTTTGTTTAAAGATTTAAAGTAA - ->human -????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CGCCTGCGGATTCTACTGGGGGCCCCTGAGCGTGCACGGGGCGCACGAGCGGCTGCGCGCCGAGCCCGTGGGCACCTTCCTGGTGCGCGACAGCCGCCAGCGGAACTGCTTTTTCGCCCTTAGCGTGAAGATGGCCTCGGGACCCACGAGCATCCGCGTGCACTTTCAGGCCGGCCGCTTTCACCTGGATGGCAGCCGCGAGAGCTTCGACTGCCTCTTCGAGCTGCTGGAGCACTACGTGGCGGCGCCGCGCCGCATGCTGGGGGCCCCGCTGCGCCAGCGCCGCGTGCGGCCGCTGCAGGAGCTGTGCCGCCAGCGCATCGTGGCCACCGTGGGCCGCGAGAACCTGGCTCGCATCCCCCTCAACCCCGTCCTCCGCGACTACCTGAGCTCCTTCCCCTTCCAGATTTGA ->chimp -??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CGTGGGCACCTTCCTGGTGCGCGACAGCCGCCA???GAACTGCTT???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GGGGCCCCGCTGCGCCAGCGCCGCGTGCGGCCGCTGCAGGAGCTGTGCCGCCAGCGCATCGTGGCTACCGTGGGCCGCGAGAA??????????ATCCCCCTCAACCCCGTCCTCCGCGACTACCTGAGCTCCTTCCCCTTCCAGATTTG? ->mouse ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTGGACGCCTGCGGCTTCTATTGGGGACCCCTGAGCGTGCACGGGGCGCACGAGCGGCTGCGTGCCGAGCCCGTGGGCACCTTCTTGGTGCGCGACAGTCGCCAACGGAACTGCTTCTTCGCGCTCAGCGTGAAGATGGCTTCGGGCCCCACGAGCATCCGCGTGCACTTCCAGGCCGGCCGCTTCCACTTGGACGGCAGCCGCGAGACCTTCGACTGCCTTTTCGAGCTGCTGGAGCACTACGTGGCGGCGCCGCGCCGCATGTTGGGGGCCCCGCTGCGCCAGCGCCGCGTGCGGCCGCTGCAGGAGCTGTGTCGCCAGCGCATCGTGGCCGCCGTGGGTCGCGAGAACCTGGCGCGCATCCCTCTTAACCCGGTACTCCGTGACTACCTGAGTTCCTTCCCCTTCCAGATCTGA - ->human -ATGGAGAGGGCTTCTAAGAATCTTAAGGGTCGGTGTACCCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAAAAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTTCGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTTGGTTCTTTTCCTATGACTCCATCAATTCCAGCTAATCCTCCCATGGCTTTCAATCCTTACATACCACATCCTGGGATGGGCCTCGTTCCTGCAGAACTTGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAATGCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAGGTTTGCCGAGAATTTCAGCGTGGAAATTGTACCCGTGGGGAGAATGATTGCCGCTATGCTCACCCTACTGATGCTTCCATGATTGAAGCGAGTGATAATACTGTGACAATCTGCATGGATTACATCAAAGGTCGATGCTCGCGGGAGAAATGCAAGTACTTTCATCCTCCTGCACACTTGCAAGCCAGACTCAAGGCAGCTCATCATCAGATGAACCATTCAGCTGCCTCTGCCATGGCCCTGCAGCCTGGTACACTGCAACTGATACCAAAGAGATCAGCACTGGAAAAGCCCAATGGTGCCACCCCGGTCTTTAATCCCACTGTTTTCCACTGCCAACAGGCTCTGACTAACCTGCAGCTCCCACAGCCGGCATTTATCCCTGCAGGGCCAATACTGTGCATGGCACCCGCTTCAAATATTGTGCCCATGATGCACGGTGCTACACCTACCACTGTGTCTGCAGCAACAACACCTGCCACCAGCGTTCCGTTCGCTGCACCAACTACAGGCAATCAG???????????? ->chimp -ATGGAGAGGGCTTCTAAGAATCTTAAGGGTCGGTGTACTCGAGAGAACTGCAAGTACCTTCACCCTCCTCCACACTTAAAAACGCAGCTGGAGATTAATGGGCGGAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTTCGCCCAGCAGATGCAGCTTATGCTCCAAAACGCTCAAATGTCATCACTT????CTTTTCCTATGACTCCATCACTTC????TAATCCTCCC????????????????????????????????????????????????????????TGTACCAAATACACCTGTTCTGATTCCTGGAAACCCACCTCTTGCAATGCCAGGAGCTGTTGGCCCAAAACTGATGCGTTCAGATAAACTGGAG???????GAGAATTTCAGCGTGGAAATTGTACCCGTGGGGAGAATGATTGCCGCTATGCTCACCCTACTGATGCTTCCATGATTGAAGCGAGTGATAATACTGTGACAATCTGCATGGATTACATCAAAG???GAT?CTCGCGGG??AAAT???AGTACTTTCATCCTCCT???CACTTG??AGCCAGACTCAAGGCAGCTCATCACCAGATGAACCATTCAGCTGCCTCTGCCATG???????????TGGTA?ACTGCAACTGATACCAAAGAGATC?????TGGAAAAGCCCAATGGTGCCACCCCGGTCTTTAATCCCACTGTTTTCCACTGCCAACAG???????????????CAGCTCCCACAGCCGGCATTTATC?????????????????????????????????????????????CCCATGATGCACGGTGCTACACCTACCACTGTGTCTGCAGCAACAACACCTGC???CAGCGTTCCGTTCGC?????????????????????????????????? ->mouse -???????????????????????????GGTCGGTGCACTCGTGAGAACTGCAAGTACCTCCACCCTCCACCGCACTTAAAGTCGCAGCTAGAAGTTAATGGGAGAAACAATCTGATTCAACAGAAGACTGCCGCAGCCATGTTCGCCCAGCACATGCAACTCATGCTGCAGAACGCTCAGATGTCATCTCTTGCGTCTTTTCCTATGAATCCATCACTTGCAGCTAATCCTGCCATGGCTTTCAATCCTTACATGACTCATCCTGGCATGGGCCTGGTTCCTGCTGAGCTTTTACCAAATGGTCCGGTTCTGATTTCTGGAAACCCTCCTCTTGCACTGCCAGGAGTTCCTGGTCCAAAGCCAATTCGTACAGATAGACTGGAGGTTTGCCGTGAATTTCAGCGTGGAAATTGTACCCGTGGGGAGAGCGAGTGCCGCTATGCTCACCCTACGGATGTTTCCATGATTGAAGTCACTGATAATTCTGTGACAATCTGCATGGATTACATTAAAGGCCGATGCTCCCGGGAGAAATGCAAGTACTTTCATCCTCCTCCCCACTTGCAGGCCAAACTCAGGGCAGCTCATCACCAGATGAACCATTCTGCTGCCAATGCAATGGCCCTGCCGCATGGTGCACTTCAACTGATACCAAAGAGGTCAGCCCTTGACAAGGCCAATGGTGCCACTCCAGTCTTTAACCCCAGTGTTTTCCACTGCCAACAGGCTCTGGCTAACATGCAGATTCCTCAGCAGGCTTTTATCCCAACAGGGCAAATACTGTGCATGACTCCTACTTCAACTTTTGTGCCCATGATGCACGGTGCTACACCTTCCACTGTGTCTACAGCAACACCACCTGCCAGCAACGTTCCCTACGTTCCAACAACTACAGGCAACCAG???????????? diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/dnds_out.tabular --- a/test-data/dnds_out.tabular +++ /dev/null @@ -1,12 +0,0 @@ -BLOCK BP S_sites NS_sites Stop_codons LogL omega omega_range AC AT CG CT GT Tree -1 1554 355.669 1129.12 1 -2747.41 0.101091 0.0764852-0.130612 1 1 1 1 1 (human:0,chimp:0.00240807,mouse:0.146665) -2 3795 924.935 2749.35 1 -5781.01 0.0179472 0.0119925-0.0256202 1 1 1 1 1 (human:0.000420081,chimp:0.00148421,mouse:0.144947) -3 1194 272.323 881.914 1 -2043.72 0.0578031 0.0372143-0.084959 1 1 1 1 1 (human:0.00284673,chimp:0.00410898,mouse:0.119894) -4 1146 248.261 850.364 1 -1871.67 0.0127675 0.00548017-0.0247362 1 1 1 1 1 (human:0,chimp:0.000930953,mouse:0.147214) -5 1500 366.374 1086.09 2 -2522.97 0.0331798 0.020375-0.0505273 1 1 1 1 1 (human:0,chimp:0.00225972,mouse:0.15608) -6 3444 824.107 2475.54 1 -5459.18 0.0439794 0.0326464-0.0577021 1 1 1 1 1 (human:0.000511634,chimp:0.00203553,mouse:0.12664) -7 2175 505.186 1587.7 0 -3307.52 0.0711476 0.0563725-0.088397 1 1 1 1 1 (human:0.00229288,chimp:0.00236918,mouse:0.226482) -8 3519 792.702 2601.36 0 -6219.39 0.0669744 0.0568959-0.0782191 1 1 1 1 1 (human:0.00102613,chimp:0.00431639,mouse:0.251285) -9 501 100.22 376.039 1 -834.329 0.130018 0.0833903-0.191879 1 1 1 1 1 (human:0,chimp:0,mouse:0.150605) -10 633 160.252 453.228 1 -618.997 0.0151077 0.00250472-0.0467226 1 1 1 1 1 (human:0,chimp:0.00611289,mouse:0.104294) -11 915 229.705 658.82 0 -1664.02 0.299399 0.227668-0.385279 1 1 1 1 1 (human:0.00457673,chimp:0,mouse:0.145584) diff -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 -r f68bd3660813e4d5024a71d84a8a8c0a24ae892a test-data/encode_1.bed --- a/test-data/encode_1.bed +++ /dev/null @@ -1,568 +0,0 @@ -chr7 26853157 26854215 EarlyRepSeg -chr7 26865558 26956110 EarlyRepSeg -chr7 26956330 26958851 EarlyRepSeg -chr7 26958893 26959464 EarlyRepSeg -chr7 26959504 26959533 EarlyRepSeg -chr7 26960356 26960376 EarlyRepSeg -chr7 26960632 26960801 EarlyRepSeg -chr7 89741530 89743766 EarlyRepSeg -chr7 89743824 89744003 EarlyRepSeg -chr7 89744088 89744106 EarlyRepSeg -chr7 89745480 89968351 EarlyRepSeg -chr7 90542632 90542691 EarlyRepSeg -chr7 113919823 113919871 EarlyRepSeg -chr7 113919935 113920029 EarlyRepSeg -chr7 113920113 113920978 EarlyRepSeg -chr7 113922569 113924554 EarlyRepSeg -chr7 113924746 113924793 EarlyRepSeg -chr7 113924833 113927725 EarlyRepSeg -chr7 113927893 113928509 EarlyRepSeg -chr7 113929396 113929453 EarlyRepSeg -chr7 113933276 114108846 EarlyRepSeg -chr7 114108947 114119346 EarlyRepSeg -chr7 114119404 114119556 EarlyRepSeg -chr7 114119621 114123541 EarlyRepSeg -chr7 114124457 114124490 EarlyRepSeg -chr7 114124634 114136954 EarlyRepSeg -chr7 114142730 114142885 EarlyRepSeg -chr7 114143714 114143737 EarlyRepSeg -chr7 114143779 114144176 EarlyRepSeg -chr7 114144305 114144327 EarlyRepSeg -chr7 114360998 114361020 EarlyRepSeg -chr7 114362526 114363858 EarlyRepSeg -chr7 115404471 116251468 EarlyRepSeg -chr7 116251612 116251638 EarlyRepSeg -chr7 116251693 116251827 EarlyRepSeg -chr7 116251956 116252352 EarlyRepSeg -chr7 116252418 116253165 EarlyRepSeg -chr7 116463012 116463121 EarlyRepSeg -chr7 116474219 116474393 EarlyRepSeg -chr7 116474517 116474771 EarlyRepSeg -chr7 116484623 116561352 EarlyRepSeg -chr7 116561778 116562791 EarlyRepSeg -chr7 116563539 116571400 EarlyRepSeg -chr7 116572311 116572335 EarlyRepSeg -chr7 116572377 116572548 EarlyRepSeg -chr7 116576381 116576667 EarlyRepSeg -chr7 116597894 116597915 EarlyRepSeg -chr7 116598129 116598237 EarlyRepSeg -chr7 116598300 116608071 EarlyRepSeg -chr7 116608165 116608209 EarlyRepSeg -chr7 116608255 116608278 EarlyRepSeg -chr7 116608335 116608527 EarlyRepSeg -chr7 116609208 116609273 EarlyRepSeg -chr7 116630981 116631297 EarlyRepSeg -chr7 116633902 116634213 EarlyRepSeg -chr7 116634270 116641382 EarlyRepSeg -chr7 116694148 116698403 EarlyRepSeg -chr7 116698511 116698606 EarlyRepSeg -chr7 116698648 116698807 EarlyRepSeg -chr7 116699036 116699669 EarlyRepSeg -chr7 116735241 116737872 EarlyRepSeg -chr7 116738045 116738948 EarlyRepSeg -chr7 116739086 116739461 EarlyRepSeg -chr7 116739526 116742149 EarlyRepSeg -chr7 116742220 116744605 EarlyRepSeg -chr7 116746201 116746659 EarlyRepSeg -chr7 116746728 116746820 EarlyRepSeg -chr7 116747018 116758597 EarlyRepSeg -chr7 116763552 116928910 EarlyRepSeg -chr7 116929761 116930077 EarlyRepSeg -chr7 116931422 116931446 EarlyRepSeg -chr6 41867303 41867713 EarlyRepSeg -chr6 41868622 41868636 EarlyRepSeg -chr6 41871084 41871127 EarlyRepSeg -chr6 41871277 41871508 EarlyRepSeg -chr6 41881436 41904567 EarlyRepSeg -chr6 74114855 74115081 EarlyRepSeg -chr6 74115174 74289952 EarlyRepSeg -chr6 108641673 108641689 EarlyRepSeg -chr6 108641837 108645076 EarlyRepSeg -chr6 108645288 108645828 EarlyRepSeg -chr6 108645850 108645872 EarlyRepSeg -chr6 108645893 108647550 EarlyRepSeg -chr6 108655265 108657582 EarlyRepSeg -chr6 108658752 108658815 EarlyRepSeg -chr6 108667835 108668566 EarlyRepSeg -chr6 108675247 108677563 EarlyRepSeg -chr6 108678755 108678800 EarlyRepSeg -chr6 108687834 108688151 EarlyRepSeg -chr6 108689330 108689377 EarlyRepSeg -chr6 108751831 108752466 EarlyRepSeg -chr6 108870546 108870611 EarlyRepSeg -chr6 132325404 132325465 EarlyRepSeg -chr6 132327970 132328191 EarlyRepSeg -chr6 132328279 132329125 EarlyRepSeg -chr6 132329408 132329455 EarlyRepSeg -chr6 132329514 132329602 EarlyRepSeg -chr6 132329683 132340765 EarlyRepSeg -chr6 132341999 132342746 EarlyRepSeg -chr6 132344613 132344841 EarlyRepSeg -chr6 132345103 132345170 EarlyRepSeg -chr6 132346006 132346044 EarlyRepSeg -chr6 132346178 132346746 EarlyRepSeg -chr6 132347078 132347478 EarlyRepSeg -chr6 132370237 132372346 EarlyRepSeg -chr6 132383528 132383567 EarlyRepSeg -chr6 132384242 132384262 EarlyRepSeg -chr6 132384405 132384422 EarlyRepSeg -chr6 132384833 132385384 EarlyRepSeg -chr6 132387114 132387150 EarlyRepSeg -chr6 132394199 132396580 EarlyRepSeg -chr5 55886021 55886041 EarlyRepSeg -chr5 55886110 55886132 EarlyRepSeg -chr5 55886176 55886195 EarlyRepSeg -chr5 55888015 55889053 EarlyRepSeg -chr5 55889099 55889140 EarlyRepSeg -chr5 55889401 55890905 EarlyRepSeg -chr5 56106962 56107249 EarlyRepSeg -chr5 56107766 56107862 EarlyRepSeg -chr5 56367460 56370292 EarlyRepSeg -chr5 56370336 56370891 EarlyRepSeg -chr5 131285263 131285306 EarlyRepSeg -chr5 131475247 131494484 EarlyRepSeg -chr5 131505619 131505861 EarlyRepSeg -chr5 131507116 131595694 EarlyRepSeg -chr5 131655935 131849308 EarlyRepSeg -chr5 131849349 131849383 EarlyRepSeg -chr5 131849499 131849515 EarlyRepSeg -chr5 131888105 132000339 EarlyRepSeg -chr5 132005729 132006017 EarlyRepSeg -chr5 132006171 132007566 EarlyRepSeg -chr5 132007757 132008189 EarlyRepSeg -chr5 132015742 132015789 EarlyRepSeg -chr5 132015951 132018096 EarlyRepSeg -chr5 132018338 132019909 EarlyRepSeg -chr5 132052942 132052981 EarlyRepSeg -chr5 132053021 132056571 EarlyRepSeg -chr5 132058138 132058229 EarlyRepSeg -chr5 132058505 132058526 EarlyRepSeg -chr5 132061788 132061810 EarlyRepSeg -chr5 132061846 132062661 EarlyRepSeg -chr5 132062832 132113831 EarlyRepSeg -chr5 132139962 132145821 EarlyRepSeg -chr5 132145885 132146737 EarlyRepSeg -chr5 132146782 132146803 EarlyRepSeg -chr5 132146845 132158072 EarlyRepSeg -chr5 132158112 132158184 EarlyRepSeg -chr5 132159741 132165336 EarlyRepSeg -chr5 132165401 132165803 EarlyRepSeg -chr5 132165876 132166736 EarlyRepSeg -chr5 132192266 132192327 EarlyRepSeg -chr5 132192395 132194449 EarlyRepSeg -chr5 132194758 132195445 EarlyRepSeg -chr5 132195811 132196282 EarlyRepSeg -chr5 132207140 132213592 EarlyRepSeg -chr5 132214738 132214752 EarlyRepSeg -chr5 132226393 132234169 EarlyRepSeg -chr5 132234504 132234598 EarlyRepSeg -chr5 132235860 132235963 EarlyRepSeg -chr5 132236046 132236459 EarlyRepSeg -chr5 132236763 132237613 EarlyRepSeg -chr5 132238255 132238299 EarlyRepSeg -chr5 132238475 132283603 EarlyRepSeg -chr5 142095059 142095166 EarlyRepSeg -chr5 142095247 142095397 EarlyRepSeg -chr5 142095465 142100861 EarlyRepSeg -chr5 142101243 142102608 EarlyRepSeg -chr5 142102655 142151401 EarlyRepSeg -chr5 142154629 142158905 EarlyRepSeg -chr5 142159158 142159198 EarlyRepSeg -chr5 142159679 142173072 EarlyRepSeg -chr18 59412370 59433985 EarlyRepSeg -chr18 59434207 59456478 EarlyRepSeg -chr18 59456699 59456831 EarlyRepSeg -chr18 59456869 59456903 EarlyRepSeg -chr18 59456922 59457354 EarlyRepSeg -chr18 59457439 59465986 EarlyRepSeg -chr18 59466027 59466067 EarlyRepSeg -chr18 59466105 59466165 EarlyRepSeg -chr18 59466225 59472274 EarlyRepSeg -chr18 59472339 59472402 EarlyRepSeg -chr18 59473339 59473490 EarlyRepSeg -chr18 59475475 59475498 EarlyRepSeg -chr18 59475900 59476000 EarlyRepSeg -chr18 59476207 59476408 EarlyRepSeg -chr18 59476471 59476911 EarlyRepSeg -chr18 59477077 59477336 EarlyRepSeg -chr18 59477401 59485966 EarlyRepSeg -chr18 59486026 59486046 EarlyRepSeg -chr18 59486215 59492264 EarlyRepSeg -chr18 59492348 59492397 EarlyRepSeg -chr18 59493339 59493451 EarlyRepSeg -chr18 59521111 59521385 EarlyRepSeg -chr18 59558120 59558177 EarlyRepSeg -chr18 59558222 59558288 EarlyRepSeg -chr2 220105509 220107457 EarlyRepSeg -chr2 234274981 234460520 EarlyRepSeg -chr1 147971142 148444534 EarlyRepSeg -chr1 148444657 148444760 EarlyRepSeg -chr1 148445123 148445166 EarlyRepSeg -chr1 148445324 148445350 EarlyRepSeg -chr1 148446462 148446660 EarlyRepSeg -chr1 148447388 148447426 EarlyRepSeg -chr1 148447762 148471133 EarlyRepSeg -chr9 128765210 128856811 EarlyRepSeg -chr9 128901865 129004365 EarlyRepSeg -chr9 129005361 129008847 EarlyRepSeg -chr9 129009370 129009735 EarlyRepSeg -chr9 129010052 129015022 EarlyRepSeg -chr9 129015082 129018165 EarlyRepSeg -chr9 129018225 129027884 EarlyRepSeg -chr9 129028821 129039792 EarlyRepSeg -chr9 129040135 129040200 EarlyRepSeg -chr9 129040288 129040309 EarlyRepSeg -chr9 129040511 129040529 EarlyRepSeg -chr9 129045169 129045941 EarlyRepSeg -chr9 129046139 129052414 EarlyRepSeg -chr9 129059485 129063706 EarlyRepSeg -chr9 129064025 129064072 EarlyRepSeg -chr9 129064243 129064284 EarlyRepSeg -chr9 129071282 129073376 EarlyRepSeg -chr9 129073850 129074365 EarlyRepSeg -chr9 129075271 129075470 EarlyRepSeg -chr9 129148128 129148471 EarlyRepSeg -chr9 129174601 129174644 EarlyRepSeg -chr9 129174683 129174867 EarlyRepSeg -chr9 129177812 129178277 EarlyRepSeg -chr9 129179593 129181321 EarlyRepSeg -chr9 129182910 129182993 EarlyRepSeg -chr9 129185792 129229546 EarlyRepSeg -chrX 122515118 122518380 EarlyRepSeg -chrX 122519180 122519262 EarlyRepSeg -chrX 122519357 122521476 EarlyRepSeg -chrX 122526240 122526737 EarlyRepSeg -chrX 122527607 122527693 EarlyRepSeg -chrX 122528249 122528336 EarlyRepSeg -chrX 122528657 122529022 EarlyRepSeg -chrX 122529666 122530817 EarlyRepSeg -chrX 122565527 122565950 EarlyRepSeg -chrX 122566173 122566198 EarlyRepSeg -chrX 122566267 122566475 EarlyRepSeg -chrX 122566527 122566817 EarlyRepSeg -chrX 122567687 122582126 EarlyRepSeg -chrX 122583489 122584103 EarlyRepSeg -chrX 122594426 122596210 EarlyRepSeg -chrX 122596274 122617296 EarlyRepSeg -chrX 122633600 122633665 EarlyRepSeg -chrX 122634493 122634584 EarlyRepSeg -chrX 122636090 122872532 EarlyRepSeg -chrX 122876952 122877037 EarlyRepSeg -chrX 122877088 122877176 EarlyRepSeg -chrX 122878185 122878198 EarlyRepSeg -chrX 122879577 122880529 EarlyRepSeg -chrX 122880573 122880754 EarlyRepSeg -chrX 122880991 122881034 EarlyRepSeg -chrX 122884162 122904171 EarlyRepSeg -chrX 122904230 122904397 EarlyRepSeg -chrX 122905605 122905631 EarlyRepSeg -chrX 122905822 122906072 EarlyRepSeg -chrX 122906141 122908153 EarlyRepSeg -chrX 122908290 122908441 EarlyRepSeg -chrX 122908471 122909074 EarlyRepSeg -chrX 122909361 122909402 EarlyRepSeg -chrX 122909482 122913104 EarlyRepSeg -chrX 122915256 122915324 EarlyRepSeg -chrX 152760672 152760721 EarlyRepSeg -chrX 152760829 152760842 EarlyRepSeg -chrX 152761258 152770914 EarlyRepSeg -chrX 152771016 152808667 EarlyRepSeg -chrX 152808758 152808842 EarlyRepSeg -chrX 152809200 152809641 EarlyRepSeg -chrX 152809809 152809850 EarlyRepSeg -chrX 152809894 152809916 EarlyRepSeg -chrX 152810266 152810965 EarlyRepSeg -chrX 152830891 152831471 EarlyRepSeg -chrX 152850880 152851459 EarlyRepSeg -chrX 152861605 152868939 EarlyRepSeg -chrX 152868998 152869602 EarlyRepSeg -chrX 152869727 152870175 EarlyRepSeg -chrX 152876992 152877431 EarlyRepSeg -chrX 152877498 152878262 EarlyRepSeg -chrX 152901180 152901356 EarlyRepSeg -chrX 152901520 152901723 EarlyRepSeg -chrX 152903274 152903322 EarlyRepSeg -chrX 152904885 152907019 EarlyRepSeg -chrX 153090357 153101014 EarlyRepSeg -chrX 153101371 153104136 EarlyRepSeg -chrX 153104196 153106352 EarlyRepSeg -chrX 153297819 153305186 EarlyRepSeg -chrX 153367214 153398065 EarlyRepSeg -chrX 153409564 153409652 EarlyRepSeg -chrX 153409708 153452751 EarlyRepSeg -chrX 153825634 153825902 EarlyRepSeg -chrX 153825944 153832126 EarlyRepSeg -chrX 153833045 153834044 EarlyRepSeg -chr13 29689066 29689271 EarlyRepSeg -chr13 29689993 29691138 EarlyRepSeg -chr13 29691184 29691786 EarlyRepSeg -chr13 29699635 29723447 EarlyRepSeg -chr13 29724097 29724150 EarlyRepSeg -chr13 29724437 29729278 EarlyRepSeg -chr13 29729324 29729541 EarlyRepSeg -chr13 29748182 29749259 EarlyRepSeg -chr13 29749301 29749322 EarlyRepSeg -chr13 29750436 29778548 EarlyRepSeg -chr13 29779059 29779318 EarlyRepSeg -chr13 29779377 29782224 EarlyRepSeg -chr13 29782457 29782521 EarlyRepSeg -chr13 29782985 29783026 EarlyRepSeg -chr13 29783068 29783105 EarlyRepSeg -chr13 29783187 29794875 EarlyRepSeg -chr13 29795145 29795419 EarlyRepSeg -chr13 29795506 29795568 EarlyRepSeg -chr13 29795610 29795657 EarlyRepSeg -chr13 29797042 29797089 EarlyRepSeg -chr13 29797248 29805175 EarlyRepSeg -chr13 29807253 29807274 EarlyRepSeg -chr13 29807727 29812203 EarlyRepSeg -chr13 29812642 29820660 EarlyRepSeg -chr13 29842265 29842438 EarlyRepSeg -chr13 29854299 29854461 EarlyRepSeg -chr13 29855916 29863126 EarlyRepSeg -chr13 29865139 29866737 EarlyRepSeg -chr13 29867798 29867842 EarlyRepSeg -chr13 29867923 29868153 EarlyRepSeg -chr13 29870372 29870486 EarlyRepSeg -chr13 29870595 29871893 EarlyRepSeg -chr13 29875493 29875515 EarlyRepSeg -chr13 29875906 29876049 EarlyRepSeg -chr13 29876280 29876544 EarlyRepSeg -chr13 29877549 29877594 EarlyRepSeg -chr13 29877640 29877755 EarlyRepSeg -chr13 29888848 29889116 EarlyRepSeg -chr13 29913298 29915450 EarlyRepSeg -chr13 29916692 29916808 EarlyRepSeg -chr13 29916871 29916912 EarlyRepSeg -chr12 38857192 38857838 EarlyRepSeg -chr12 38858064 38859517 EarlyRepSeg -chr11 64242393 64242795 EarlyRepSeg -chr11 64244176 64244321 EarlyRepSeg -chr11 64297901 64321446 EarlyRepSeg -chr11 116114836 116128702 EarlyRepSeg -chr11 116134467 116135228 EarlyRepSeg -chr11 116256326 116256395 EarlyRepSeg -chr11 116256453 116256519 EarlyRepSeg -chr11 116257093 116257138 EarlyRepSeg -chr11 116257203 116257403 EarlyRepSeg -chr11 116259428 116260093 EarlyRepSeg -chr11 116280588 116294899 EarlyRepSeg -chr11 116294934 116295981 EarlyRepSeg -chr11 116296783 116298100 EarlyRepSeg -chr11 116298577 116298670 EarlyRepSeg -chr11 116298713 116299250 EarlyRepSeg -chr11 116320712 116321239 EarlyRepSeg -chr11 116326943 116398307 EarlyRepSeg -chr11 116398468 116398525 EarlyRepSeg -chr11 116398574 116398772 EarlyRepSeg -chr11 116398840 116399053 EarlyRepSeg -chr11 116400410 116401850 EarlyRepSeg -chr11 116401898 116402342 EarlyRepSeg -chr11 116402425 116403775 EarlyRepSeg -chr11 116406023 116415188 EarlyRepSeg -chr11 116415423 116417404 EarlyRepSeg -chr11 116417596 116441864 EarlyRepSeg -chr11 116443999 116444201 EarlyRepSeg -chr11 116444843 116445008 EarlyRepSeg -chr11 116445046 116448354 EarlyRepSeg -chr11 116448391 116448434 EarlyRepSeg -chr11 116448672 116448715 EarlyRepSeg -chr11 116461947 116462084 EarlyRepSeg -chr22 30129315 30200724 EarlyRepSeg -chr22 30200767 30200791 EarlyRepSeg -chr22 30200897 30205649 EarlyRepSeg -chr22 30230684 30231848 EarlyRepSeg -chr22 30239701 30239723 EarlyRepSeg -chr22 30240912 30240933 EarlyRepSeg -chr22 30241666 30241903 EarlyRepSeg -chr22 30243634 30243709 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-chr21 32793700 32794302 EarlyRepSeg -chr21 32795603 32795626 EarlyRepSeg -chr21 32823257 32834186 EarlyRepSeg -chr21 32835989 32836025 EarlyRepSeg -chr21 32838501 32838523 EarlyRepSeg -chr21 32838557 32838598 EarlyRepSeg -chr21 32838643 32838756 EarlyRepSeg -chr21 32838799 32838988 EarlyRepSeg -chr21 32839538 32877989 EarlyRepSeg -chr21 32878079 32878098 EarlyRepSeg -chr21 32878144 32878203 EarlyRepSeg -chr21 32878246 32878267 EarlyRepSeg -chr21 32879333 32879475 EarlyRepSeg -chr21 32879966 32879983 EarlyRepSeg -chr21 32912504 32915865 EarlyRepSeg -chr21 32932980 32967601 EarlyRepSeg -chr21 32967643 33018889 EarlyRepSeg -chr21 33024974 33025376 EarlyRepSeg -chr21 33026349 33028938 EarlyRepSeg -chr21 33031749 33032829 EarlyRepSeg -chr21 33524233 33524260 EarlyRepSeg -chr21 33524376 33524397 EarlyRepSeg -chr21 33524744 33524770 EarlyRepSeg -chr21 33550677 33553459 EarlyRepSeg -chr21 33553902 33558482 EarlyRepSeg -chr21 33580367 33580388 EarlyRepSeg -chr21 33580473 33581913 EarlyRepSeg 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-chr21 39506003 39506049 EarlyRepSeg -chr21 39506091 39506345 EarlyRepSeg -chr21 39506424 39506484 EarlyRepSeg -chr21 39506703 39507084 EarlyRepSeg -chr21 39507119 39630459 EarlyRepSeg -chr21 39630770 39631537 EarlyRepSeg -chr21 39631609 39632660 EarlyRepSeg -chr21 39634408 39634612 EarlyRepSeg -chr21 39634672 39637021 EarlyRepSeg -chr21 39637718 39637740 EarlyRepSeg -chr21 39638104 39639318 EarlyRepSeg -chr21 39639514 39639764 EarlyRepSeg -chr21 39639832 39640101 EarlyRepSeg -chr21 39640247 39640471 EarlyRepSeg -chr21 39642473 39642490 EarlyRepSeg -chr21 39642699 39643256 EarlyRepSeg -chr21 39643292 39643361 EarlyRepSeg -chr20 33304928 33309185 EarlyRepSeg -chr20 33331535 33662613 EarlyRepSeg -chr20 33663823 33784967 EarlyRepSeg -chr8 119109535 119109779 EarlyRepSeg -chr8 119133176 119314664 EarlyRepSeg -chr8 119314783 119314804 EarlyRepSeg -chr8 119315080 119315854 EarlyRepSeg -chr8 119316284 119317841 EarlyRepSeg -chr8 119317881 119319990 EarlyRepSeg -chr8 119321302 119322430 EarlyRepSeg -chr8 119322628 119322752 EarlyRepSeg This diff is so big that we needed to truncate the remainder. 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: guerler: Upload: Use find from underscore
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/40b9b13ec62b/ Changeset: 40b9b13ec62b User: guerler Date: 2014-02-17 18:58:39 Summary: Upload: Use find from underscore Affected #: 4 files diff -r a67b8cdce345bef55e349641445598e7db735a1a -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -321,7 +321,7 @@ var $el = $(this.el).find('#extension-info'); var extension = this.model.get('extension'); var title = this.select_extension.text(); - var description = Utils.findPair(this.app.list_extensions, 'id', extension); + var description = _.findWhere(this.app.list_extensions, {'id': extension}); // create popup if (!this.extension_popup) { diff -r a67b8cdce345bef55e349641445598e7db735a1a -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:h.find("#genome"),value:f.model.get("genome")});this.model.set("genome",f.select_genome.value());this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:h.find("#extension"),value:f.model.get("extension")});this.model.set("extension",f.select_extension.value());h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var f=this.model.get("genome");this.select_genome.value(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();var g=d.findPair(this.app.list_extensions,"id",i);if(!this.extension_popup){this.extension_popup=new c.View({placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(g));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_templateDescription:function(g){if(g.description){var f=g.description;if(g.description_url){f+=' (<a href="'+g.description_url+'" target="_blank">read more</a>)'}return f}else{return"There is no description available for this file extension."}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:h.find("#genome"),value:f.model.get("genome")});this.model.set("genome",f.select_genome.value());this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:h.find("#extension"),value:f.model.get("extension")});this.model.set("extension",f.select_extension.value());h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var f=this.model.get("genome");this.select_genome.value(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();var g=_.findWhere(this.app.list_extensions,{id:i});if(!this.extension_popup){this.extension_popup=new c.View({placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(g));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_templateDescription:function(g){if(g.description){var f=g.description;if(g.description_url){f+=' (<a href="'+g.description_url+'" target="_blank">read more</a>)'}return f}else{return"There is no description available for this file extension."}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file diff -r a67b8cdce345bef55e349641445598e7db735a1a -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(c){function f(k,j,i){var l=new XMLHttpRequest();l.open("GET",k,true);l.setRequestHeader("Accept","application/json");l.setRequestHeader("Cache-Control","no-cache");l.setRequestHeader("X-Requested-With","XMLHttpRequest");l.onloadend=function(){var m=l.status;if(m==200){try{response=jQuery.parseJSON(l.responseText)}catch(n){response=l.responseText}j&&j(response)}else{i&&i(m)}};l.send()}function b(l,i){var j=$('<div class="'+l+'"></div>');j.appendTo(":eq(0)");var k=j.css(i);j.remove();return k}function a(i){if(!$('link[href^="'+i+'"]').length){$('<link href="'+galaxy_config.root+i+'" rel="stylesheet">').appendTo("head")}}function h(i,j){if(i){return c.defaults(i,j)}else{return j}}function d(j,l){var k="";if(j>=100000000000){j=j/100000000000;k="TB"}else{if(j>=100000000){j=j/100000000;k="GB"}else{if(j>=100000){j=j/100000;k="MB"}else{if(j>=100){j=j/100;k="KB"}else{if(j>0){j=j*10;k="b"}else{return"<strong>-</strong>"}}}}}var i=(Math.round(j)/10);if(l){return i+" "+k}else{return"<strong>"+i+"</strong> "+k}}function e(){return(new Date().getTime()).toString(36)}function g(j,l,n){for(var k in j){var m=j[k];if(m[l]==n){return m}}return{}}return{cssLoadFile:a,cssGetAttribute:b,jsonFromUrl:f,merge:h,bytesToString:d,uuid:e,findPair:g}}); \ No newline at end of file +define(["libs/underscore"],function(c){function f(j,i,h){var k=new XMLHttpRequest();k.open("GET",j,true);k.setRequestHeader("Accept","application/json");k.setRequestHeader("Cache-Control","no-cache");k.setRequestHeader("X-Requested-With","XMLHttpRequest");k.onloadend=function(){var l=k.status;if(l==200){try{response=jQuery.parseJSON(k.responseText)}catch(m){response=k.responseText}i&&i(response)}else{h&&h(l)}};k.send()}function b(k,h){var i=$('<div class="'+k+'"></div>');i.appendTo(":eq(0)");var j=i.css(h);i.remove();return j}function a(h){if(!$('link[href^="'+h+'"]').length){$('<link href="'+galaxy_config.root+h+'" rel="stylesheet">').appendTo("head")}}function g(h,i){if(h){return c.defaults(h,i)}else{return i}}function d(i,k){var j="";if(i>=100000000000){i=i/100000000000;j="TB"}else{if(i>=100000000){i=i/100000000;j="GB"}else{if(i>=100000){i=i/100000;j="MB"}else{if(i>=100){i=i/100;j="KB"}else{if(i>0){i=i*10;j="b"}else{return"<strong>-</strong>"}}}}}var h=(Math.round(i)/10);if(k){return h+" "+j}else{return"<strong>"+h+"</strong> "+j}}function e(){return(new Date().getTime()).toString(36)}return{cssLoadFile:a,cssGetAttribute:b,jsonFromUrl:f,merge:g,bytesToString:d,uuid:e}}); \ No newline at end of file diff -r a67b8cdce345bef55e349641445598e7db735a1a -r 40b9b13ec62b43d83e96d6624edbaea967da82a6 static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -96,17 +96,6 @@ return (new Date().getTime()).toString(36); }; -// find in dict -function findPair(arr, key, val) { - for (var i in arr) { - var item = arr[i]; - if (item[key] == val) { - return item; - } - } - return {}; -} - // return return { cssLoadFile : cssLoadFile, @@ -114,8 +103,7 @@ jsonFromUrl : jsonFromUrl, merge : merge, bytesToString: bytesToString, - uuid: uuid, - findPair: findPair + uuid: uuid }; }); 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.

1 0

commit/galaxy-central: dan: Add a script to check toolshed dependency files for broken/invalid download URLs.
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a67b8cdce345/ Changeset: a67b8cdce345 User: dan Date: 2014-02-17 18:51:34 Summary: Add a script to check toolshed dependency files for broken/invalid download URLs. Affected #: 1 file diff -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b -r a67b8cdce345bef55e349641445598e7db735a1a scripts/tool_shed/check_download_urls.py --- /dev/null +++ b/scripts/tool_shed/check_download_urls.py @@ -0,0 +1,39 @@ +#!/usr/bin/env python +##Dan Blankenberg +##Script that checks toolshed tags to see if URLs are accessible. +##Does not currently handle 'download_binary' + +import os +import sys +from optparse import OptionParser +import xml.etree.ElementTree as ET +import urllib2 + +FILENAMES = [ 'tool_dependencies.xml' ] +ACTION_TYPES = [ 'download_by_url', 'download_file' ] + +def main(): + parser = OptionParser() + parser.add_option( '-d', '--directory', dest='directory', action='store', type="string", default='.', help='Root directory' ) + + ( options, args ) = parser.parse_args() + + for (dirpath, dirnames, filenames) in os.walk( options.directory ): + for filename in filenames: + if filename in FILENAMES: + path = os.path.join( dirpath, filename ) + try: + tree = ET.parse( path ) + root = tree.getroot() + for action_type in ACTION_TYPES: + for element in root.findall( ".//action[@type='%s']" % action_type ): + url = element.text.strip() + try: + urllib2.urlopen( urllib2.Request( url ) ) + except Exception, e: + print "Bad URL '%s' in file '%s': %s" % ( url, path, e ) + except Exception, e: + print "Unable to check XML file '%s': %s" % ( path, e ) + +if __name__ == "__main__": + main() 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.

1 0

commit/galaxy-central: carlfeberhard: UI: add peek-based column selection control; Scatterplot: use peek-based control for selection of x, y, id axes
by commits-noreply＠bitbucket.org 17 Feb '14

17 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6353214a32ee/ Changeset: 6353214a32ee User: carlfeberhard Date: 2014-02-17 18:11:04 Summary: UI: add peek-based column selection control; Scatterplot: use peek-based control for selection of x, y, id axes Affected #: 8 files diff -r 3e7842687fd3bde8ab47007e91fcf705df1e66db -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars --- a/config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars +++ b/config/plugins/visualizations/scatterplot/src/handlebars/datacontrol.handlebars @@ -1,55 +1,24 @@ <p class="help-text"> - Use the following controls to change the data used by the chart. + Use the following control to change which columns are used by the chart. Click any cell + from the last three rows of the table to select the column for the appropriate data. Use the 'Draw' button to render (or re-render) the chart with the current settings. </p> -{{! column selector containers }} -<div class="column-select"> - <label>Data column for X: </label> - <select name="xColumn"> - {{#each numericColumns}} - <option value="{{index}}">{{name}}</option> - {{/each}} - </select> -</div> -<div class="column-select"> - <label>Data column for Y: </label> - <select name="yColumn"> - {{#each numericColumns}} - <option value="{{index}}">{{name}}</option> - {{/each}} - </select> +<ul class="help-text" style="margin-left: 8px"> + <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li> + <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li> + <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point. + It may be useful to select unique or categorical identifiers here (such as gene ids). + </li> +</ul> + +<div class="column-selection"> + <pre class="peek">{{{ peek }}}</pre></div> -{{! optional id column }} -<div id="include-id"> - <label for="include-id-checkbox">Include a third column as data point IDs?</label> - <input type="checkbox" name="include-id" id="include-id-checkbox" /> - <p class="help-text-small"> - These will be displayed (along with the x and y values) when you hover over - a data point. - </p> -</div> -<div class="column-select" style="display: none"> - <label for="ID-select">Data column for IDs: </label> - <select name="idColumn"> - {{#each allColumns}} - <option value="{{index}}">{{name}}</option> - {{/each}} - </select> -</div> - -{{! if we're using generic column selection names ('column 1') - allow the user to use the first line }} -<div id="first-line-header" style="display: none;"> - <p>Possible headers: {{ possibleHeaders }} - </p> - <label for="first-line-header-checkbox">Use the above as column headers?</label> - <input type="checkbox" name="include-id" id="first-line-header-checkbox" - {{#if usePossibleHeaders }}checked="true"{{/if}}/> - <p class="help-text-small"> - It looks like Galaxy couldn't get proper column headers for this data. - Would you like to use the column headers above as column names to select columns? - </p> -</div> +<p class="help-text help-text-small"> + <b>Note</b>: If it can be determined from the dataset's filetype that column is not numeric, that + column choice may be disabled for either the x or y axis. +</p><button class="render-button btn btn-primary active">Draw</button> diff -r 3e7842687fd3bde8ab47007e91fcf705df1e66db -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js --- a/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js +++ b/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js @@ -78,73 +78,62 @@ return this; }, + /** get an object with arrays keyed with possible column types (numeric, text, all) + * and if metadata_column_types is set on the dataset, add the indeces of each + * column into the appropriate array. + * Used to disable certain columns from being selected for x, y axes. + */ + _getColumnIndecesByType : function(){ + //TODO: not sure these contraints are necc. now + var types = { + numeric : [], + text : [], + all : [] + }; + _.each( this.dataset.metadata_column_types || [], function( type, i ){ + if( type === 'int' || type === 'float' ){ + types.numeric.push( i ); + } else if( type === 'str' || type === 'list' ){ + types.text.push( i ); + } + types.all.push( i ); + }); + if( types.numeric.length < 2 ){ + types.numeric = []; + } + //console.log( 'types:', JSON.stringify( types ) ); + return types; + }, + /** controls for which columns are used to plot datapoints (and ids/additional info to attach if desired) */ _render_dataControl : function( $where ){ - //TODO: better handling of missing column names, column types $where = $where || this.$el; var editor = this, - dataset = this.dataset, - column_names = dataset.metadata_column_names || [], - config = this.model.get( 'config' ); - //console.log( 'metadata_column_types:', this.dataset.metadata_column_types ); - //console.log( 'metadata_column_names:', this.dataset.metadata_column_names ); - -//TODO: to peek based control - var numericColumns = [], - allColumns = _.map( dataset.metadata_column_types, function( type, i ){ - // save column data for select rendering, adding metadata name if available in dataset - var column = { index: i, type: type, name: ( column_names[ i ] || ( 'column ' + ( i + 1 )) ) }; - // also add column to numerics if numeric type - if( ( column.type === 'int' ) || ( column.type === 'float' ) ){ - numericColumns.push( column ); - } - return column; - }); - if( numericColumns.length < 2 ){ - numericColumns = allColumns; - } - //console.log( 'allColumns:', allColumns ); - //console.log( 'numericColumns:', numericColumns ); + //column_names = dataset.metadata_column_names || [], + config = this.model.get( 'config' ), + columnTypes = this._getColumnIndecesByType(); // render the html var $dataControl = $where.find( '.tab-pane#data-control' ); $dataControl.html( ScatterplotConfigEditor.templates.dataControl({ - allColumns : allColumns, - numericColumns : numericColumns + peek : this.dataset.peek })); -//TODO: column selection boilerplate - // preset to column selectors if they were passed in the config in the query string; set up events - var newConfig = { - xColumn : ( _.isFinite( config.xColumn ) )? ( config.xColumn ): ( numericColumns[0].index ), - yColumn : ( _.isFinite( config.yColumn ) )? ( config.yColumn ): ( numericColumns[1].index ), - idColumn : allColumns[0].index - }; - // use an idColumn from the config or attempt to get one different from the numeric - if( _.isFinite( config.idColumn ) ){ - newConfig.idColumn = config.idColumn; - } else { - if( allColumns.length > 2 ){ - var uniqueCol = _.find( allColumns, function( column, i ){ - return i !== newConfig.xColumn && i !== newConfig.yColumn; - }); - newConfig.idColumn = uniqueCol.index; - } - } - config = this.model.set( 'config', newConfig, { silent: true }).get( 'config' ); + $dataControl.find( '.peek' ).peekControl({ + controls : [ + { label: 'X Column', id: 'xColumn', selected: config.xColumn, disabled: columnTypes.text }, + { label: 'Y Column', id: 'yColumn', selected: config.yColumn, disabled: columnTypes.text }, + { label: 'ID Column', id: 'idColumn', selected: config.idColumn } + ] + //renameColumns : true - $dataControl.find( '[name="xColumn"]' ).val( config.xColumn ).on( 'change', function(){ - editor.model.set( 'config', { xColumn: Number( $( this ).val() ) }); + }).on( 'peek-control.change', function( ev, data ){ + //console.info( 'new selection:', data ); + editor.model.set( 'config', data ); + + }).on( 'peek-control.rename', function( ev, data ){ + //console.info( 'new column names', data ); }); - $dataControl.find( '[name="yColumn"]' ).val( config.yColumn ).on( 'change', function(){ - editor.model.set( 'config', { yColumn: Number( $( this ).val() ) }); - }); - $dataControl.find( 'select[name="idColumn"]' ).val( config.idColumn ).on( 'change', function(){ - editor.model.set( 'config', { idColumn: Number( $( this ).val() ) }); - }); - if( config.idColumn !== undefined ){ - $dataControl.find( '#include-id-checkbox' ).prop( 'checked', true ).trigger( 'change' ); - } $dataControl.find( '[title]' ).tooltip(); return $dataControl; diff -r 3e7842687fd3bde8ab47007e91fcf705df1e66db -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b config/plugins/visualizations/scatterplot/static/scatterplot-edit.js --- a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js +++ b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js @@ -1,1 +1,1 @@ -function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.x.ticks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.y.ticks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("class","axis-label").text(b.x.label).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("class","axis-label").text(b.y.label).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="'+i((f=b.x,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+i((f=b.y,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){function f(a,b){var d,e="";return e+='\n <option value="',(d=c.index)?d=d.call(a,{hash:{},data:b}):(d=a.index,d=typeof d===j?d.apply(a):d),e+=k(d)+'">',(d=c.name)?d=d.call(a,{hash:{},data:b}):(d=a.name,d=typeof d===j?d.apply(a):d),e+=k(d)+"</option>\n "}function g(){return'checked="true"'}this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var h,i="",j="function",k=this.escapeExpression,l=this;return i+='<p class="help-text">\n Use the following controls to change the data used by the chart.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n\n<div class="column-select">\n <label>Data column for X: </label>\n <select name="xColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n<div class="column-select">\n <label>Data column for Y: </label>\n <select name="yColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n</div>\n<div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="idColumn">\n ',h=c.each.call(b,b.allColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="first-line-header" style="display: none;">\n <p>Possible headers: ',(h=c.possibleHeaders)?h=h.call(b,{hash:{},data:e}):(h=b.possibleHeaders,h=typeof h===j?h.apply(b):h),i+=k(h)+'\n </p>\n <label for="first-line-header-checkbox">Use the above as column headers?</label>\n <input type="checkbox" name="include-id" id="first-line-header-checkbox"\n ',h=c["if"].call(b,b.usePossibleHeaders,{hash:{},inverse:l.noop,fn:l.program(3,g,e),data:e}),(h||0===h)&&(i+=h),i+='/>\n <p class="help-text-small">\n It looks like Galaxy couldn\'t get proper column headers for this data.\n Would you like to use the column headers above as column names to select columns?\n </p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div id="data-control" class="scatterplot-config-control tab-pane active">\n \n </div>\n \n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n \n </div>\n\n \n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'});var ScatterplotConfigEditor=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),this.log(this+".initialize, attributes:",a),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.log("dataset:",this.dataset),this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.dataset,d=c.metadata_column_names||[],e=this.model.get("config"),f=[],g=_.map(c.metadata_column_types,function(a,b){var c={index:b,type:a,name:d[b]||"column "+(b+1)};return("int"===c.type||"float"===c.type)&&f.push(c),c});f.length<2&&(f=g);var h=a.find(".tab-pane#data-control");h.html(ScatterplotConfigEditor.templates.dataControl({allColumns:g,numericColumns:f}));var i={xColumn:_.isFinite(e.xColumn)?e.xColumn:f[0].index,yColumn:_.isFinite(e.yColumn)?e.yColumn:f[1].index,idColumn:g[0].index};if(_.isFinite(e.idColumn))i.idColumn=e.idColumn;else if(g.length>2){var j=_.find(g,function(a,b){return b!==i.xColumn&&b!==i.yColumn});i.idColumn=j.index}return e=this.model.set("config",i,{silent:!0}).get("config"),h.find('[name="xColumn"]').val(e.xColumn).on("change",function(){b.model.set("config",{xColumn:Number($(this).val())})}),h.find('[name="yColumn"]').val(e.yColumn).on("change",function(){b.model.set("config",{yColumn:Number($(this).val())})}),h.find('select[name="idColumn"]').val(e.idColumn).on("change",function(){b.model.set("config",{idColumn:Number($(this).val())})}),void 0!==e.idColumn&&h.find("#include-id-checkbox").prop("checked",!0).trigger("change"),h.find("[title]").tooltip(),h},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.x.label,e=b.y.label,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}}); \ No newline at end of file +function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.x.ticks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.y.ticks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("class","axis-label").text(b.x.label).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("class","axis-label").text(b.y.label).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="'+i((f=b.x,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+i((f=b.y,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function";return g+='<p class="help-text">\n Use the following control to change which columns are used by the chart. Click any cell\n from the last three rows of the table to select the column for the appropriate data.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<ul class="help-text" style="margin-left: 8px">\n <li><b>X Column</b>: which column values will be used for the x axis of the chart.</li>\n <li><b>Y Column</b>: which column values will be used for the y axis of the chart.</li>\n <li><b>ID Column</b>: an additional column value displayed when the user hovers over a data point.\n It may be useful to select unique or categorical identifiers here (such as gene ids).\n </li>\n</ul>\n\n<div class="column-selection">\n <pre class="peek">',(f=c.peek)?f=f.call(b,{hash:{},data:e}):(f=b.peek,f=typeof f===h?f.apply(b):f),(f||0===f)&&(g+=f),g+='</pre>\n</div>\n\n<p class="help-text help-text-small">\n <b>Note</b>: If it can be determined from the dataset\'s filetype that column is not numeric, that\n column choice may be disabled for either the x or y axis.\n</p>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div id="data-control" class="scatterplot-config-control tab-pane active">\n \n </div>\n \n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n \n </div>\n\n \n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'});var ScatterplotConfigEditor=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),this.log(this+".initialize, attributes:",a),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.log("dataset:",this.dataset),this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_getColumnIndecesByType:function(){var a={numeric:[],text:[],all:[]};return _.each(this.dataset.metadata_column_types||[],function(b,c){"int"===b||"float"===b?a.numeric.push(c):("str"===b||"list"===b)&&a.text.push(c),a.all.push(c)}),a.numeric.length<2&&(a.numeric=[]),a},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.model.get("config"),d=this._getColumnIndecesByType(),e=a.find(".tab-pane#data-control");return e.html(ScatterplotConfigEditor.templates.dataControl({peek:this.dataset.peek})),e.find(".peek").peekControl({controls:[{label:"X Column",id:"xColumn",selected:c.xColumn,disabled:d.text},{label:"Y Column",id:"yColumn",selected:c.yColumn,disabled:d.text},{label:"ID Column",id:"idColumn",selected:c.idColumn}]}).on("peek-control.change",function(a,c){b.model.set("config",c)}).on("peek-control.rename",function(){}),e.find("[title]").tooltip(),e},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.x.label,e=b.y.label,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}}); \ No newline at end of file diff -r 3e7842687fd3bde8ab47007e91fcf705df1e66db -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b config/plugins/visualizations/scatterplot/templates/scatterplot.mako --- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako +++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako @@ -87,7 +87,7 @@ model : model, dataset : hdaJson }).render(); - //window.editor = editor; + window.editor = editor; $( '.chart-header h2' ).click( function(){ var returned = prompt( 'Enter a new title:' ); diff -r 3e7842687fd3bde8ab47007e91fcf705df1e66db -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -1299,3 +1299,310 @@ }); }()); + +//============================================================================== +/** Column selection using the peek display as the control. + * Adds rows to the bottom of the peek with clickable areas in each cell + * to allow the user to select columns. + * Column selection can be limited to a single column or multiple. + * (Optionally) adds a left hand column of column selection prompts. + * (Optionally) allows the column headers to be clicked/renamed + * and set to some initial value. + * (Optionally) hides comment rows. + * (Optionally) allows pre-selecting and disabling certain columns for + * each row control. + * + * Construct by selecting a peek table to be used with jQuery and + * calling 'peekControl' with options. + * Options must include a 'controls' array and can include other options + * listed below. + * @example: + * $( 'pre.peek' ).peekControl({ + * columnNames : ["Chromosome", "Start", "Base", "", "", "Qual" ], + * controls : [ + * { label: 'X Column', id: 'xColumn' }, + * { label: 'Y Column', id: 'yColumn', selected: 2 }, + * { label: 'ID Column', id: 'idColumn', selected: 4, disabled: [ 1, 5 ] }, + * { label: 'Heatmap', id: 'heatmap', selected: [ 2, 4 ], disabled: [ 0, 1 ], multiselect: true, + * selectedText: 'Included', unselectedText: 'Excluded' } + * ], + * renameColumns : true, + * hideCommentRows : true, + * includePrompts : true, + * topLeftContent : 'Data sample:' + * }).on( 'peek-control.change', function( ev, selection ){ + * console.info( 'new selection:', selection ); + * //{ yColumn: 2 } + * }).on( 'peek-control.rename', function( ev, names ){ + * console.info( 'column names', names ); + * //[ 'Bler', 'Start', 'Base', '', '', 'Qual' ] + * }); + * + * An event is fired when column selection is changed and the event + * is passed an object in the form: { the row id : the new selection value }. + * An event is also fired when the table headers are re-named and + * is passed the new array of column names. + */ +(function(){ + + /** option defaults */ + var defaults = { + /** does this control allow renaming headers? */ + renameColumns : false, + /** does this control allow renaming headers? */ + columnNames : [], + /** the comment character used by the peek's datatype */ + commentChar : '#', + /** should comment rows be shown or hidden in the peek */ + hideCommentRows : false, + /** should a column of row control prompts be used */ + includePrompts : true, + /** what is the content of the top left cell (often a title) */ + topLeftContent : 'Columns:' + }, + /** the string of the event fired when a control row changes */ + CHANGE_EVENT = 'peek-control.change', + /** the string of the event fired when a column is renamed */ + RENAME_EVENT = 'peek-control.rename', + /** class added to the pre.peek element (to allow css on just the control) */ + PEEKCONTROL_CLASS = 'peek-control', + /** class added to the control rows */ + ROW_CLASS = 'control', + /** class added to the left-hand cells that serve as row prompts */ + PROMPT_CLASS = 'control-prompt', + /** class added to selected _cells_/tds */ + SELECTED_CLASS = 'selected', + /** class added to disabled/un-clickable cells/tds */ + DISABLED_CLASS = 'disabled', + /** class added to the clickable surface within a cell to select it */ + BUTTON_CLASS = 'button', + /** class added to peek table header (th) cells to indicate they can be clicked and are renamable */ + RENAMABLE_HEADER_CLASS = 'renamable-header', + /** the data key used for each cell to store the column index ('data-...') */ + COLUMN_INDEX_DATA_KEY = 'column-index', + /** renamable header data key used to store the column name (w/o the number and dot: '1.Bler') */ + COLUMN_NAME_DATA_KEY = 'column-name'; + + //TODO: not happy with pure functional here - rows should polymorph (multi, single, etc.) + //TODO: needs clean up, move handlers to outer scope + + // ........................................................................ + /** validate the control data sent in for each row */ + function validateControl( control ){ + if( control.disabled && jQuery.type( control.disabled ) !== 'array' ){ + throw new Error( '"disabled" must be defined as an array of indeces: ' + JSON.stringify( control ) ); + } + if( control.multiselect && control.selected && jQuery.type( control.selected ) !== 'array' ){ + throw new Error( 'Mulitselect rows need an array for "selected": ' + JSON.stringify( control ) ); + } + if( !control.label || !control.id ){ + throw new Error( 'Peek controls need a label and id for each control row: ' + JSON.stringify( control ) ); + } + if( control.disabled && control.disabled.indexOf( control.selected ) !== -1 ){ + throw new Error( 'Selected column is in the list of disabled columns: ' + JSON.stringify( control ) ); + } + return control; + } + + /** build the inner control surface (i.e. button-like) */ + function buildButton( control, columnIndex ){ + return $( '<div/>' ).addClass( BUTTON_CLASS ).text( control.label ); + } + + /** build the basic (shared) cell structure */ + function buildControlCell( control, columnIndex ){ + var $td = $( '<td/>' ) + .html( buildButton( control, columnIndex ) ) + .attr( 'data-' + COLUMN_INDEX_DATA_KEY, columnIndex ); + + // disable if index in disabled array + if( control.disabled && control.disabled.indexOf( columnIndex ) !== -1 ){ + $td.addClass( DISABLED_CLASS ); + } + return $td; + } + + /** set the text of the control based on selected/un */ + function setSelectedText( $cell, control, columnIndex ){ + var $button = $cell.children( '.' + BUTTON_CLASS ); + if( $cell.hasClass( SELECTED_CLASS ) ){ + $button.html( ( control.selectedText !== undefined )?( control.selectedText ):( control.label ) ); + } else { + $button.html( ( control.unselectedText !== undefined )?( control.unselectedText ):( control.label ) ); + } + } + + /** build a cell for a row that only allows one selection */ + function buildSingleSelectCell( control, columnIndex ){ + // only one selection - selected is single index + var $cell = buildControlCell( control, columnIndex ); + if( control.selected === columnIndex ){ + $cell.addClass( SELECTED_CLASS ); + } + setSelectedText( $cell, control, columnIndex ); + + // only add the handler to non-disabled controls + if( !$cell.hasClass( DISABLED_CLASS ) ){ + $cell.click( function selectClick( ev ){ + var $cell = $( this ); + // don't re-select or fire event if already selected + if( !$cell.hasClass( SELECTED_CLASS ) ){ + // only one can be selected - remove selected on all others, add it here + var $otherSelected = $cell.parent().children( '.' + SELECTED_CLASS ).removeClass( SELECTED_CLASS ); + $otherSelected.each( function(){ + setSelectedText( $( this ), control, columnIndex ); + }); + + $cell.addClass( SELECTED_CLASS ); + setSelectedText( $cell, control, columnIndex ); + + // fire the event from the table itself, passing the id and index of selected + var eventData = {}, + key = $cell.parent().attr( 'id' ), + val = $cell.data( COLUMN_INDEX_DATA_KEY ); + eventData[ key ] = val; + $cell.parents( '.peek' ).trigger( CHANGE_EVENT, eventData ); + } + }); + } + return $cell; + } + + /** build a cell for a row that allows multiple selections */ + function buildMultiSelectCell( control, columnIndex ){ + var $cell = buildControlCell( control, columnIndex ); + // multiple selection - selected is an array + if( control.selected && control.selected.indexOf( columnIndex ) !== -1 ){ + $cell.addClass( SELECTED_CLASS ); + } + setSelectedText( $cell, control, columnIndex ); + + // only add the handler to non-disabled controls + if( !$cell.hasClass( DISABLED_CLASS ) ){ + $cell.click( function multiselectClick( ev ){ + var $cell = $( this ); + // can be more than one selected - toggle selected on this cell + $cell.toggleClass( SELECTED_CLASS ); + setSelectedText( $cell, control, columnIndex ); + var selectedColumnIndeces = $cell.parent().find( '.' + SELECTED_CLASS ).map( function( i, e ){ + return $( e ).data( COLUMN_INDEX_DATA_KEY ); + }); + // fire the event from the table itself, passing the id and index of selected + var eventData = {}, + key = $cell.parent().attr( 'id' ), + val = jQuery.makeArray( selectedColumnIndeces ); + eventData[ key ] = val; + $cell.parents( '.peek' ).trigger( CHANGE_EVENT, eventData ); + }); + } + return $cell; + } + + /** iterate over columns in peek and create a control for each */ + function buildControlCells( count, control ){ + var $cells = []; + // build a control for each column - using a build fn based on control + for( var columnIndex=0; columnIndex<count; columnIndex+=1 ){ + $cells.push( control.multiselect? buildMultiSelectCell( control, columnIndex ) + : buildSingleSelectCell( control, columnIndex ) ); + } + return $cells; + } + + /** build a row of controls for the peek */ + function buildControlRow( cellCount, control, includePrompts ){ + var $controlRow = $( '<tr/>' ).attr( 'id', control.id ).addClass( ROW_CLASS ); + if( includePrompts ){ + var $promptCell = $( '<td/>' ).addClass( PROMPT_CLASS ).text( control.label + ':' ); + $controlRow.append( $promptCell ); + } + $controlRow.append( buildControlCells( cellCount, control ) ); + return $controlRow; + } + + // ........................................................................ + /** add to the peek, using options for configuration, return the peek */ + function peekControl( options ){ + options = jQuery.extend( true, {}, defaults, options ); + + var $peek = $( this ).addClass( PEEKCONTROL_CLASS ), + $peektable = $peek.find( 'table' ), + // get the size of the tables - width and height, number of comment rows + columnCount = $peektable.find( 'th' ).size(), + rowCount = $peektable.find( 'tr' ).size(), + // get the rows containing text starting with the comment char (also make them grey) + $commentRows = $peektable.find( 'td[colspan]' ).map( function( e, i ){ + var $this = $( this ); + if( $this.text() && $this.text().match( new RegExp( '^' + options.commentChar ) ) ){ + return $( this ).css( 'color', 'grey' ).parent().get(0); + } + return null; + }); + + // should comment rows in the peek be hidden? + if( options.hideCommentRows ){ + $commentRows.hide(); + rowCount -= $commentRows.size(); + } + //console.debug( 'rowCount:', rowCount, 'columnCount:', columnCount, '$commentRows:', $commentRows ); + + // should a first column of control prompts be added? + if( options.includePrompts ){ + var $topLeft = $( '<th/>' ).addClass( 'top-left' ).text( options.topLeftContent ) + .attr( 'rowspan', rowCount ); + $peektable.find( 'tr' ).first().prepend( $topLeft ); + } + + // save either the options column name or the parsed text of each column header in html5 data attr and text + var $headers = $peektable.find( 'th:not(.top-left)' ).each( function( i, e ){ + var $this = $( this ), + // can be '1.name' or '1' + text = $this.text().replace( /^\d+\.*/, '' ), + name = options.columnNames[ i ] || text; + $this.attr( 'data-' + COLUMN_NAME_DATA_KEY, name ) + .text( ( i + 1 ) + (( name )?( '.' + name ):( '' )) ); + }); + + // allow renaming of columns when the header is clicked + if( options.renameColumns ){ + $headers.addClass( RENAMABLE_HEADER_CLASS ) + .click( function renameColumn(){ + // prompt for new name + var $this = $( this ), + index = $this.index() + ( options.includePrompts? 0: 1 ), + prevName = $this.data( COLUMN_NAME_DATA_KEY ), + newColumnName = prompt( 'New column name:', prevName ); + if( newColumnName !== null && newColumnName !== prevName ){ + // set the new text and data + $this.text( index + ( newColumnName?( '.' + newColumnName ):'' ) ) + .data( COLUMN_NAME_DATA_KEY, newColumnName ) + .attr( 'data-', COLUMN_NAME_DATA_KEY, newColumnName ); + // fire event for new column names + var columnNames = jQuery.makeArray( + $this.parent().children( 'th:not(.top-left)' ).map( function(){ + return $( this ).data( COLUMN_NAME_DATA_KEY ); + })); + $this.parents( '.peek' ).trigger( RENAME_EVENT, columnNames ); + } + }); + } + + // build a row for each control + options.controls.forEach( function( control, i ){ + validateControl( control ); + var $controlRow = buildControlRow( columnCount, control, options.includePrompts ); + $peektable.find( 'tbody' ).append( $controlRow ); + }); + return this; + } + + // ........................................................................ + // as jq plugin + jQuery.fn.extend({ + peekControl : function $peekControl( options ){ + return this.map( function(){ + return peekControl.call( this, options ); + }); + } + }); +}()); diff -r 3e7842687fd3bde8ab47007e91fcf705df1e66db -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.create=function _create(b,a){return new PopupMenu(b,a)};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((!a.disabled&&a.target)?(' target="'+a.target+'"'):("")),' href="',((!a.disabled&&a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}(function(){function a(j,p){var d=27,m=13,c=$(j),e=true,g={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(q){},minSearchLen:0,escWillClear:true,oninit:function(){}};function i(q){var r=$(this).parent().children("input");r.val("");r.trigger("clear:searchInput");p.onclear()}function o(r,q){$(this).trigger("search:searchInput",q);if(typeof p.onfirstsearch==="function"&&e){e=false;p.onfirstsearch(q)}else{p.onsearch(q)}}function f(){return['<input type="text" name="',p.name,'" placeholder="',p.placeholder,'" ','class="search-query ',p.classes,'" ',"/>"].join("")}function l(){return $(f()).focus(function(q){$(this).select()}).keyup(function(r){if(r.which===d&&p.escWillClear){i.call(this,r)}else{var q=$(this).val();if((r.which===m)||(p.minSearchLen&&q.length>=p.minSearchLen)){o.call(this,r,q)}else{if(!q.length){i.call(this,r)}}}}).val(p.initialVal)}function k(){return $(['<span class="search-clear fa fa-times-circle" ','title="',_l("clear search (esc)"),'"></span>'].join("")).tooltip({placement:"bottom"}).click(function(q){i.call(this,q)})}function n(){return $(['<span class="search-loading fa fa-spinner fa-spin" ','title="',_l("loading..."),'"></span>'].join("")).hide().tooltip({placement:"bottom"})}function h(){c.find(".search-loading").toggle();c.find(".search-clear").toggle()}if(jQuery.type(p)==="string"){if(p==="toggle-loading"){h()}return c}if(jQuery.type(p)==="object"){p=jQuery.extend(true,{},g,p)}return c.addClass("search-input").prepend([l(),k(),n()])}jQuery.fn.extend({searchInput:function b(c){return this.each(function(){return a(this,c)})}})}());(function(){function b(m,l){this.currModeIndex=0;return this.init(m,l)}b.prototype.DATA_KEY="mode-button";b.prototype.defaults={modes:[{mode:"default"}]};b.prototype.init=function f(m,l){l=l||{};this.$element=$(m);this.options=jQuery.extend(true,{},this.defaults,l);var o=this;this.$element.click(function n(p){o.callModeFn();o._incModeIndex();$(this).html(o.options.modes[o.currModeIndex].html)});this.currModeIndex=0;if(this.options.initialMode){this.currModeIndex=this._getModeIndex(this.options.initialMode)}return this};b.prototype._getModeIndex=function j(l){for(var m=0;m<this.options.modes.length;m+=1){if(this.options.modes[m].mode===l){return m}}throw new Error("mode not found: "+l)};b.prototype.getCurrMode=function a(){return this.options.modes[this.currModeIndex]};b.prototype.getMode=function g(l){if(!l){return this.getCurrMode()}return this.options.modes[(this._getModeIndex(l))]};b.prototype.hasMode=function k(l){return !!this.getMode(l)};b.prototype.currentMode=function e(){return this.options.modes[this.currModeIndex]};b.prototype.setMode=function c(m){var l=this.getMode(m);this.$element.html(l.html||null);return this};b.prototype._incModeIndex=function d(){this.currModeIndex+=1;if(this.currModeIndex>=this.options.modes.length){this.currModeIndex=0}return this};b.prototype.callModeFn=function h(l){var m=this.getMode(l).onclick;if(m&&jQuery.type(m==="function")){return m.call(this)}return undefined};jQuery.fn.extend({modeButton:function i(m){var l=jQuery.makeArray(arguments).slice(1);return this.map(function(){var p=$(this),o=p.data("mode-button");if(jQuery.type(m)==="object"){o=new b(p,m);p.data("mode-button",o)}else{if(o&&jQuery.type(m)==="string"){var n=o[m];if(jQuery.type(n)==="function"){return n.apply(o,l)}}else{if(o){return o}}}return this})}})}());function dropDownSelect(b,c){c=c||((!_.isEmpty(b))?(b[0]):(""));var a=$(['<div class="dropdown-select btn-group">','<button type="button" class="btn btn-default">','<span class="dropdown-select-selected">'+c+"</span>","</button>","</div>"].join("\n"));if(b&&b.length>1){a.find("button").addClass("dropdown-toggle").attr("data-toggle","dropdown").append(' <span class="caret"></span>');a.append(['<ul class="dropdown-menu" role="menu">',_.map(b,function(e){return['<li><a href="javascript:void(0)">',e,"</a></li>"].join("")}).join("\n"),"</ul>"].join("\n"))}function d(g){var h=$(this),f=h.parents(".dropdown-select"),e=h.text();f.find(".dropdown-select-selected").text(e);f.trigger("change.dropdown-select",e)}a.find("a").click(d);return a}(function(){function e(k,j){return this.init(k,j)}e.prototype.DATA_KEY="filter-control";e.prototype.init=function g(k,j){j=j||{filters:[]};this.$element=$(k).addClass("filter-control btn-group");this.options=jQuery.extend(true,{},this.defaults,j);this.currFilter=this.options.filters[0];return this.render()};e.prototype.render=function d(){this.$element.empty().append([this._renderKeySelect(),this._renderOpSelect(),this._renderValueInput()]);return this};e.prototype._renderKeySelect=function a(){var j=this;var k=this.options.filters.map(function(l){return l.key});this.$keySelect=dropDownSelect(k,this.currFilter.key).addClass("filter-control-key").on("change.dropdown-select",function(m,l){j.currFilter=_.findWhere(j.options.filters,{key:l});j.render()._triggerChange()});return this.$keySelect};e.prototype._renderOpSelect=function i(){var j=this,k=this.currFilter.ops;this.$opSelect=dropDownSelect(k,k[0]).addClass("filter-control-op").on("change.dropdown-select",function(m,l){j._triggerChange()});return this.$opSelect};e.prototype._renderValueInput=function c(){var j=this;if(this.currFilter.values){this.$valueSelect=dropDownSelect(this.currFilter.values,this.currFilter.values[0]).on("change.dropdown-select",function(l,k){j._triggerChange()})}else{this.$valueSelect=$("<input/>").addClass("form-control").on("change",function(k,l){j._triggerChange()})}this.$valueSelect.addClass("filter-control-value");return this.$valueSelect};e.prototype.val=function b(){var k=this.$element.find(".filter-control-key .dropdown-select-selected").text(),m=this.$element.find(".filter-control-op .dropdown-select-selected").text(),j=this.$element.find(".filter-control-value"),l=(j.hasClass("dropdown-select"))?(j.find(".dropdown-select-selected").text()):(j.val());return{key:k,op:m,value:l}};e.prototype._triggerChange=function h(){this.$element.trigger("change.filter-control",this.val())};jQuery.fn.extend({filterControl:function f(k){var j=jQuery.makeArray(arguments).slice(1);return this.map(function(){var n=$(this),m=n.data(e.prototype.DATA_KEY);if(jQuery.type(k)==="object"){m=new e(n,k);n.data(e.prototype.DATA_KEY,m)}if(m&&jQuery.type(k)==="string"){var l=m[k];if(jQuery.type(l)==="function"){return l.apply(m,j)}}return this})}})}());(function(){function i(o,n){this.numPages=null;this.currPage=0;return this.init(o,n)}i.prototype.DATA_KEY="pagination";i.prototype.defaults={startingPage:0,perPage:20,totalDataSize:null,currDataSize:null};i.prototype.init=function g(n,o){o=o||{};this.$element=n;this.options=jQuery.extend(true,{},this.defaults,o);this.currPage=this.options.startingPage;if(this.options.totalDataSize!==null){this.numPages=Math.ceil(this.options.totalDataSize/this.options.perPage);if(this.currPage>=this.numPages){this.currPage=this.numPages-1}}this.$element.data(i.prototype.DATA_KEY,this);this._render();return this};function m(n){return $(['<li><a href="javascript:void(0);">',n,"</a></li>"].join(""))}i.prototype._render=function e(){if(this.options.totalDataSize===0){return this}if(this.numPages===1){return this}if(this.numPages>0){this._renderPages();this._scrollToActivePage()}else{this._renderPrevNext()}return this};i.prototype._renderPrevNext=function b(){var o=this,p=m("Prev"),n=m("Next"),q=$("<ul/>").addClass("pagination pagination-prev-next");if(this.currPage===0){p.addClass("disabled")}else{p.click(function(){o.prevPage()})}if((this.numPages&&this.currPage===(this.numPages-1))||(this.options.currDataSize&&this.options.currDataSize<this.options.perPage)){n.addClass("disabled")}else{n.click(function(){o.nextPage()})}this.$element.html(q.append([p,n]));return this.$element};i.prototype._renderPages=function a(){var n=this,q=$("<div>").addClass("pagination-scroll-container"),s=$("<ul/>").addClass("pagination pagination-page-list"),r=function(t){n.goToPage($(this).data("page"))};for(var o=0;o<this.numPages;o+=1){var p=m(o+1).attr("data-page",o).click(r);if(o===this.currPage){p.addClass("active")}s.append(p)}return this.$element.html(q.html(s))};i.prototype._scrollToActivePage=function l(){var p=this.$element.find(".pagination-scroll-container");if(!p.size()){return this}var o=this.$element.find("li.active"),n=p.width()/2;p.scrollLeft(p.scrollLeft()+o.position().left-n);return this};i.prototype.goToPage=function j(n){if(n<=0){n=0}if(this.numPages&&n>=this.numPages){n=this.numPages-1}if(n===this.currPage){return this}this.currPage=n;this.$element.trigger("pagination.page-change",this.currPage);this._render();return this};i.prototype.prevPage=function c(){return this.goToPage(this.currPage-1)};i.prototype.nextPage=function h(){return this.goToPage(this.currPage+1)};i.prototype.page=function f(){return this.currPage};i.create=function k(n,o){return new i(n,o)};jQuery.fn.extend({pagination:function d(o){var n=jQuery.makeArray(arguments).slice(1);if(jQuery.type(o)==="object"){return this.map(function(){i.create($(this),o);return this})}var q=$(this[0]),r=q.data(i.prototype.DATA_KEY);if(r){if(jQuery.type(o)==="string"){var p=r[o];if(jQuery.type(p)==="function"){return p.apply(r,n)}}else{return r}}return undefined}})}()); \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li 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a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.create=function _create(b,a){return new PopupMenu(b,a)};PopupMenu.make_popupmenu=function(b,c){var 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H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file diff -r 3e7842687fd3bde8ab47007e91fcf705df1e66db -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1396,6 +1396,17 @@ .pagination-scroll-container .pagination-page-list>li:first-child>a,.pagination-scroll-container .pagination-page-list>li:first-child>span{border-radius:0px;border-left:0px} .pagination-scroll-container .pagination-page-list>li:last-child>a,.pagination-scroll-container .pagination-page-list>li:last-child>span{border-radius:0px} .pagination-scroll-container .pagination-page-list>li>a{float:none;position:static;border:1px solid #BFBFBF;border-width:0px 0px 0px 1px} +.peek-control{border-radius:3px;border:1px solid #5f6990} +.peek-control td,th{padding:4px 10px 4px 4px} +.peek-control th:last-child{width:100%} +.peek-control .top-left{width:10%;white-space:normal;vertical-align:top;text-align:right;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;font-weight:normal} +.peek-control .renamable-header:hover{background-color:black} +.peek-control .control td.control-prompt{background-color:#5f6990;padding:0px 4px 0px 8px;text-align:right;color:white} +.peek-control .control td{padding:1px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;color:grey} +.peek-control .control td .button{min-width:28px;border:1px solid grey;border-radius:3px;padding:4px;color:grey} +.peek-control .control td:hover .button{background-color:#EEE;border:1px solid black;cursor:pointer;color:black} +.peek-control .control td.disabled .button,.peek-control .control td.disabled:hover .button{background-color:transparent;border:1px solid #CCC;cursor:not-allowed;color:#CCC} +.peek-control .control td.selected .button{background-color:black;border:1px solid black;color:white} div.metadataForm{border:solid #aaaaaa 1px} div.metadataFormTitle{font-weight:bold;padding:5px;padding-left:10px;padding-right:10px;background:#cccccc;background-repeat:repeat-x;background-position:top;border-bottom:solid #aaaaaa 1px} div.metadataFormBody{background:#FFFFFF;padding:5px 0} diff -r 3e7842687fd3bde8ab47007e91fcf705df1e66db -r 6353214a32ee96343f8a3e9e25e9e5b2f9517d9b static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -544,6 +544,76 @@ } +// ---------------------------------------------------------------------------- peek-based column chooser +.peek-control { + border-radius: 3px; + border: 1px solid rgb(95, 105, 144); +} + +.peek-control td, th { + padding: 4px 10px 4px 4px; +} + +.peek-control th:last-child { + width: 100%; +} + +.peek-control .top-left { + width: 10%; + white-space: normal; + vertical-align: top; + text-align: right; + font-family: "Lucida Grande", verdana, arial, helvetica, sans-serif; + font-weight: normal; +} + +.peek-control .renamable-header:hover { + background-color: black; +} + +.peek-control .control td.control-prompt { + background-color: rgb(95, 105, 144); + padding: 0px 4px 0px 8px; + text-align: right; + color: white; +} + +.peek-control .control td { + padding: 1px; + font-family: "Lucida Grande", verdana, arial, helvetica, sans-serif; + color: grey; +} + +.peek-control .control td .button { + min-width: 28px; + border: 1px solid grey; + border-radius: 3px; + padding: 4px; + color: grey; +} + +.peek-control .control td:hover .button { + background-color: #EEE; + border: 1px solid black; + cursor: pointer; + color: black; +} + +.peek-control .control td.disabled .button, +.peek-control .control td.disabled:hover .button { + background-color: transparent; + border: 1px solid #CCC; + cursor: not-allowed; + color: #CCC; +} + +.peek-control .control td.selected .button { + background-color: black; + border: 1px solid black; + color: white; +} + + // ==== Tool form styles ==== div.metadataForm { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Config: Add ‘datatypes_disable_auto’ option to universe configuration
by commits-noreply＠bitbucket.org 15 Feb '14

15 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3e7842687fd3/ Changeset: 3e7842687fd3 User: guerler Date: 2014-02-15 08:06:57 Summary: Config: Add ‘datatypes_disable_auto’ option to universe configuration Affected #: 8 files diff -r 72eec07ef71833f797c7e279a6c27c4e8a24535c -r 3e7842687fd3bde8ab47007e91fcf705df1e66db static/scripts/mvc/ui/ui-select.js --- a/static/scripts/mvc/ui/ui-select.js +++ b/static/scripts/mvc/ui/ui-select.js @@ -8,7 +8,8 @@ optionsDefault: { css : '', placeholder : 'No data available', - data : [] + data : [], + value : null }, // initialize @@ -54,17 +55,14 @@ // get current id/value var after = this._getValue(); - if(after === undefined) { - return null; - } else { - // fire onchange - if ((after != before && this.options.onchange)) { - this.options.onchange(after); - } + + // fire onchange + if ((after != before && this.options.onchange)) { + this.options.onchange(after); + } - // return current value - return after; - } + // return current value + return after; }, // label @@ -133,28 +131,18 @@ // refresh _refresh: function() { - - // link select data - var select_data = this.select_data; - if (!select_data || select_data.length == 0) { - select_data = []; - } - // selected var selected = this._getValue(); // add select2 data this.$el.select2({ - data : select_data, + data : this.select_data, containerCssClass : this.options.css, placeholder : this.options.placeholder }); - // select - var index = this._getIndex(selected); - if (index != -1) { - this._setValue(selected); - } + // select previous value (if exists) + this._setValue(selected); }, // get index @@ -177,6 +165,12 @@ // set value _setValue: function(new_value) { + var index = this._getIndex(new_value); + if (index == -1) { + if (this.select_data.length > 0) { + new_value = this.select_data[0].id; + } + } this.$el.select2('val', new_value); }, diff -r 72eec07ef71833f797c7e279a6c27c4e8a24535c -r 3e7842687fd3bde8ab47007e91fcf705df1e66db static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -71,6 +71,9 @@ container: it.find('#genome'), value: self.model.get('genome') }); + + // initialize genome + this.model.set('genome', self.select_genome.value()); // select extension this.select_extension = new Select.View({ @@ -83,6 +86,9 @@ value: self.model.get('extension') }); + // initialize extension + this.model.set('extension', self.select_extension.value()); + // // ui events // diff -r 72eec07ef71833f797c7e279a6c27c4e8a24535c -r 3e7842687fd3bde8ab47007e91fcf705df1e66db static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -42,15 +42,18 @@ upload_size: 0, // extension types - list_extensions :[{ - id : 'auto', - text : 'Auto-detect', - description : 'The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.' - }], + list_extensions :[], // genomes list_genomes : [], + // datatype placeholder for auto-detection + auto: { + id : 'auto', + text : 'Auto-detect', + description : 'This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.' + }, + // collection collection : new UploadModel.Collection(), @@ -75,7 +78,12 @@ initialize : function(options) { // link this var self = this; - + + // read in options + if (options) { + this.options = _.defaults(options, this.options); + } + // wait for galaxy history panel (workaround due to the use of iframes) if (!Galaxy.currHistoryPanel || !Galaxy.currHistoryPanel.model) { window.setTimeout(function() { self.initialize() }, 500) @@ -122,12 +130,13 @@ // sort self.list_extensions.sort(function(a, b) { - if (a.id == 'auto') - return -1; - if (b.id == 'auto') - return 1; return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; }); + + // add auto field + if (!self.options.datatypes_disable_auto) { + self.list_extensions.unshift(self.auto); + } }); // load genomes @@ -146,11 +155,6 @@ }); }); - // read in options - if (options) { - this.options = _.defaults(options, this.options); - } - // events this.collection.on('remove', function(item) { self._eventRemove(item); diff -r 72eec07ef71833f797c7e279a6c27c4e8a24535c -r 3e7842687fd3bde8ab47007e91fcf705df1e66db static/scripts/packed/mvc/ui/ui-select.js --- a/static/scripts/packed/mvc/ui/ui-select.js +++ b/static/scripts/packed/mvc/ui/ui-select.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[]},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if(e===undefined){return null}else{if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e}},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var e=this.select_data;if(!e||e.length==0){e=[]}var d=this._getValue();this.$el.select2({data:e,containerCssClass:this.options.css,placeholder:this.options.placeholder});var c=this._getIndex(d);if(c!=-1){this._setValue(d)}},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(c){this.$el.select2("val",c)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{css:"",placeholder:"No data available",data:[],value:null},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.options.container.append(this.$el);this.select_data=this.options.data;this._refresh();if(this.options.value){this._setValue(this.options.value)}var c=this;if(this.options.onchange){this.$el.on("change",function(){c.options.onchange(c.value())})}},value:function(c){var d=this._getValue();if(c!==undefined){this._setValue(c)}var e=this._getValue();if((e!=d&&this.options.onchange)){this.options.onchange(e)}return e},text:function(){return this.$el.select2("data").text},disabled:function(){return !this.$el.select2("enable")},enable:function(){this.$el.select2("enable",true)},disable:function(){this.$el.select2("enable",false)},add:function(c){this.select_data.push({id:c.id,text:c.text});this._refresh()},del:function(d){var c=this._getIndex(d);if(c!=-1){this.select_data.splice(c,1);this._refresh()}},remove:function(){this.$el.select2("destroy")},update:function(c){this.select_data=[];for(var d in c.data){this.select_data.push(c.data[d])}this._refresh()},_refresh:function(){var c=this._getValue();this.$el.select2({data:this.select_data,containerCssClass:this.options.css,placeholder:this.options.placeholder});this._setValue(c)},_getIndex:function(d){for(var c in this.select_data){if(this.select_data[c].id==d){return c}}return -1},_getValue:function(){return this.$el.select2("val")},_setValue:function(d){var c=this._getIndex(d);if(c==-1){if(this.select_data.length>0){d=this.select_data[0].id}}this.$el.select2("val",d)},_template:function(c){return'<input type="hidden"/>'}});return{View:b}}); \ No newline at end of file diff -r 72eec07ef71833f797c7e279a6c27c4e8a24535c -r 3e7842687fd3bde8ab47007e91fcf705df1e66db static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:h.find("#genome"),value:f.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:h.find("#extension"),value:f.model.get("extension")});h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var f=this.model.get("genome");this.select_genome.value(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();var g=d.findPair(this.app.list_extensions,"id",i);if(!this.extension_popup){this.extension_popup=new c.View({placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(g));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_templateDescription:function(g){if(g.description){var f=g.description;if(g.description_url){f+=' (<a href="'+g.description_url+'" target="_blank">read more</a>)'}return f}else{return"There is no description available for this file extension."}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:h.find("#genome"),value:f.model.get("genome")});this.model.set("genome",f.select_genome.value());this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:h.find("#extension"),value:f.model.get("extension")});this.model.set("extension",f.select_extension.value());h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var f=this.model.get("genome");this.select_genome.value(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();var g=d.findPair(this.app.list_extensions,"id",i);if(!this.extension_popup){this.extension_popup=new c.View({placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(g));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_templateDescription:function(g){if(g.description){var f=g.description;if(g.description_url){f+=' (<a href="'+g.description_url+'" target="_blank">read more</a>)'}return f}else{return"There is no description available for this file extension."}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file diff -r 72eec07ef71833f797c7e279a6c27c4e8a24535c -r 3e7842687fd3bde8ab47007e91fcf705df1e66db static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect",description:"The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){if(l.id=="auto"){return -1}if(k.id=="auto"){return 1}return l.id>k.id?1:l.id<k.id?-1:0})});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[],list_genomes:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(i){this.options=_.defaults(i,this.options)}if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0});if(!h.options.datatypes_disable_auto){h.list_extensions.unshift(h.auto)}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file diff -r 72eec07ef71833f797c7e279a6c27c4e8a24535c -r 3e7842687fd3bde8ab47007e91fcf705df1e66db templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -54,6 +54,7 @@ 'active_view' : active_view, 'ftp_upload_dir' : app.config.get("ftp_upload_dir", None), 'ftp_upload_site' : app.config.get("ftp_upload_site", None), + 'datatypes_disable_auto' : app.config.get_bool("datatypes_disable_auto", False), ## user details 'user' : { diff -r 72eec07ef71833f797c7e279a6c27c4e8a24535c -r 3e7842687fd3bde8ab47007e91fcf705df1e66db universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -174,6 +174,9 @@ # Galaxy. #datatypes_config_file = datatypes_conf.xml +# Disable the 'Auto-detect' option for file uploads +#datatypes_disable_auto = True + # Visualizations config directory: where to look for individual visualization plugins. # The path is relative to the Galaxy root dir. To use an absolute path begin the path # with '/'. 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.

1 0

commit/galaxy-central: guerler: Datatypes: Add datatype description to xml, Upload: Load description from xml
by commits-noreply＠bitbucket.org 15 Feb '14

15 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72eec07ef718/ Changeset: 72eec07ef718 User: guerler Date: 2014-02-15 06:06:32 Summary: Datatypes: Add datatype description to xml, Upload: Load description from xml Affected #: 12 files diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -1,13 +1,13 @@ <?xml version="1.0"?><datatypes><registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> - <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true"/> - <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false"/> + <datatype extension="ab1" type="galaxy.datatypes.binary:Ab1" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Ab1"/> + <datatype extension="afg" type="galaxy.datatypes.assembly:Amos" display_in_upload="false" /><datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true" /><datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true" /> - <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true"/> + <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/><datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/> - <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true"> + <datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"><converter file="bam_to_bai.xml" target_datatype="bai"/><converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/><display file="ucsc/bam.xml" /> @@ -15,7 +15,7 @@ <display file="igv/bam.xml" /><display file="igb/bam.xml" /></datatype> - <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true"> + <datatype extension="bed" type="galaxy.datatypes.interval:Bed" display_in_upload="true" description="BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Bed"><converter file="bed_to_gff_converter.xml" target_datatype="gff"/><converter file="bed_to_bgzip_converter.xml" target_datatype="bgzip"/><converter file="bed_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/> @@ -56,20 +56,20 @@ <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/><datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576" /><datatype extension="data_manager_json" type="galaxy.datatypes.data:Text" mimetype="application/json" subclass="True" display_in_upload="False"/> - <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true"> + <datatype extension="fasta" type="galaxy.datatypes.sequence:Fasta" display_in_upload="true" description="A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than ('>') symbol in the first column. All lines should be shorter than 80 characters." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fasta"><converter file="fasta_to_tabular_converter.xml" target_datatype="tabular"/><converter file="fasta_to_bowtie_base_index_converter.xml" target_datatype="bowtie_base_index"/><converter file="fasta_to_bowtie_color_index_converter.xml" target_datatype="bowtie_color_index"/><converter file="fasta_to_2bit.xml" target_datatype="twobit"/><converter file="fasta_to_len.xml" target_datatype="len"/></datatype> - <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true"> + <datatype extension="fastq" type="galaxy.datatypes.sequence:Fastq" display_in_upload="true" description="FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Fastq"><converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/></datatype><datatype extension="fastqsanger" type="galaxy.datatypes.sequence:FastqSanger" display_in_upload="true"><converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/></datatype> - <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true"> + <datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa"><converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/></datatype><datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true"> @@ -84,7 +84,7 @@ <datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"></datatype> - <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true"> + <datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true" description="GFF lines have nine required fields that must be tab-separated." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF"><converter file="gff_to_bed_converter.xml" target_datatype="bed"/><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> @@ -92,7 +92,7 @@ <display file="ensembl/ensembl_gff.xml" inherit="True"/></datatype> - <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true"/> + <datatype extension="gff3" type="galaxy.datatypes.interval:Gff3" display_in_upload="true" description="The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#GFF3"/><datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/><datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/><datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"> @@ -102,7 +102,7 @@ <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /><datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> - <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"> + <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." ><converter file="interval_to_bed_converter.xml" target_datatype="bed"/><converter file="interval_to_bedstrict_converter.xml" target_datatype="bedstrict"/><converter file="interval_to_bed6_converter.xml" target_datatype="bed6"/> @@ -139,8 +139,8 @@ <datatype extension="eps" type="galaxy.datatypes.images:Eps" mimetype="image/eps"/><datatype extension="rast" type="galaxy.datatypes.images:Rast" mimetype="image/rast"/><datatype extension="laj" type="galaxy.datatypes.images:Laj"/> - <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true"/> - <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true"> + <datatype extension="lav" type="galaxy.datatypes.sequence:Lav" display_in_upload="true" description="Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.." /> + <datatype extension="maf" type="galaxy.datatypes.sequence:Maf" display_in_upload="true" description="TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated 'variable=value' pairs. There should be no white space surrounding the '='." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#MAF"><converter file="maf_to_fasta_converter.xml" target_datatype="fasta"/><converter file="maf_to_interval_converter.xml" target_datatype="interval"/></datatype> @@ -168,14 +168,14 @@ <converter file="sam_to_bam.xml" target_datatype="bam"/><converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/></datatype> - <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> - <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true" description="A binary file in 'Standard Flowgram Format' with a '.sff' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Sff"/><datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/><datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> - <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/> + <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" description="Any data in tab delimited format (tabular)." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29"/><datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/> - <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true" description="Any text file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text"/><datatype extension="linecount" type="galaxy.datatypes.data:LineCount" display_in_upload="false"/><datatype extension="memexml" type="galaxy.datatypes.xml:MEMEXml" mimetype="application/xml" display_in_upload="true"/><datatype extension="cisml" type="galaxy.datatypes.xml:CisML" mimetype="application/xml" display_in_upload="true"/> @@ -191,7 +191,7 @@ </datatype><datatype extension="bcf" type="galaxy.datatypes.binary:Binary" subclass="True" display_in_upload="True"/><datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="false"/> - <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"> + <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true" description="The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Wig"><converter file="wig_to_bigwig_converter.xml" target_datatype="bigwig"/><converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c lib/galaxy/webapps/galaxy/api/datatypes.py --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -18,12 +18,25 @@ GET /api/datatypes Return an object containing upload datatypes. """ + extension_only = asbool( kwd.get( 'extension_only', True ) ) upload_only = asbool( kwd.get( 'upload_only', True ) ) try: - if upload_only: - return trans.app.datatypes_registry.upload_file_formats + if extension_only: + if upload_only: + return trans.app.datatypes_registry.upload_file_formats + else: + return [ ext for ext in trans.app.datatypes_registry.datatypes_by_extension ] else: - return [ ext for ext in trans.app.datatypes_registry.datatypes_by_extension ] + rval = [] + for elem in trans.app.datatypes_registry.datatype_elems: + if not asbool(elem.get('display_in_upload')) and upload_only: + continue + keys = ['extension', 'description', 'description_url'] + dictionary = {} + for key in keys: + dictionary[key] = elem.get(key) + rval.append(dictionary) + return rval except Exception, exception: log.error( 'could not get datatypes: %s', str( exception ), exc_info=True ) trans.response.status = 500 diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/scripts/mvc/upload/upload-extensions.js --- a/static/scripts/mvc/upload/upload-extensions.js +++ /dev/null @@ -1,110 +0,0 @@ -// dependencies -define([], function() { - -var dictionary = { - - auto : { - text: 'The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed' - }, - - ab1 : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Ab1', - text: 'A binary sequence file in \'ab1\' format with a \'.ab1\' file extension. You must manually select this \'File Format\' when uploading the file.' - }, - - axt : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Axt', - text: 'blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields.' - }, - - bam : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#BAM', - text: 'A binary file compressed in the BGZF format with a \'.bam\' file extension.' - }, - - bed : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Bed', - text: 'BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd.' - }, - - fasta : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Fasta', - text: 'A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters.' - }, - - fastq : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Fastq', - text: 'FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. ' - }, - - fastqsolexa : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa', - text: 'FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file.' - }, - - gff : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#GFF', - text: 'GFF lines have nine required fields that must be tab-separated.' - }, - - gff3 : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#GFF3', - text: 'The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats.' - }, - - interval : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#GFF3', - text: 'File must start with definition line in the following format (columns may be in any order).' - }, - - lav : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#GFF3', - text: 'Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav..' - }, - - maf : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#MAF', - text: 'TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value" pairs. There should be no white space surrounding the "=".' - }, - - scf : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Scf', - text: 'A binary sequence file in \'scf\' format with a \'.scf\' file extension. You must manually select this \'File Format\' when uploading the file.' - }, - - sff : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Sff', - text: 'A binary file in \'Standard Flowgram Format\' with a \'.sff\' file extension.' - }, - - tabular : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29', - text: 'Any data in tab delimited format (tabular).' - }, - - wig : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Wig', - text: 'The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track.' - }, - - txt : { - url : 'https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text', - text: 'Any text file.' - }, - -}; - -// create description content -return function(key) { - var description = dictionary[key]; - if (description) { - var tmpl = description.text; - if (description.url) { - tmpl += ' (<a href="' + description.url + '" target="_blank">read more</a>)'; - } - return tmpl; - } else { - return 'There is no description available for this file extension.'; - } -} -}); diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/scripts/mvc/upload/upload-row.js --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -1,14 +1,12 @@ // dependencies define(['utils/utils', 'mvc/upload/upload-model', - 'mvc/upload/upload-extensions', 'mvc/upload/upload-settings', 'mvc/ui/ui-popover', 'mvc/ui/ui-select'], function( Utils, UploadModel, - UploadExtensions, UploadSettings, Popover, Select @@ -317,11 +315,11 @@ var $el = $(this.el).find('#extension-info'); var extension = this.model.get('extension'); var title = this.select_extension.text(); + var description = Utils.findPair(this.app.list_extensions, 'id', extension); // create popup if (!this.extension_popup) { this.extension_popup = new Popover.View({ - content: UploadExtensions(extension), placement: 'bottom', container: $el }); @@ -331,7 +329,7 @@ if (!this.extension_popup.visible) { this.extension_popup.title(title); this.extension_popup.empty(); - this.extension_popup.append(UploadExtensions(extension)); + this.extension_popup.append(this._templateDescription(description)); this.extension_popup.show(); } else { this.extension_popup.hide(); @@ -352,7 +350,20 @@ this.settings.hide(); } }, - + + // template + _templateDescription: function(options) { + if (options.description) { + var tmpl = options.description; + if (options.description_url) { + tmpl += ' (<a href="' + options.description_url + '" target="_blank">read more</a>)'; + } + return tmpl; + } else { + return 'There is no description available for this file extension.'; + } + }, + // template _template: function(options) { diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/scripts/mvc/upload/upload-view.js --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -42,7 +42,11 @@ upload_size: 0, // extension types - list_extensions :[{id: 'auto', text: 'Auto-detect'}], + list_extensions :[{ + id : 'auto', + text : 'Auto-detect', + description : 'The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed.' + }], // genomes list_genomes : [], @@ -105,14 +109,25 @@ // load extension var self = this; - Utils.jsonFromUrl(galaxy_config.root + "api/datatypes?upload_only=True", + Utils.jsonFromUrl(galaxy_config.root + "api/datatypes?extension_only=False", function(datatypes) { for (key in datatypes) { self.list_extensions.push({ - id : datatypes[key], - text : datatypes[key] + id : datatypes[key].extension, + text : datatypes[key].extension, + description : datatypes[key].description, + description_url : datatypes[key].description_url }); } + + // sort + self.list_extensions.sort(function(a, b) { + if (a.id == 'auto') + return -1; + if (b.id == 'auto') + return 1; + return a.id > b.id ? 1 : a.id < b.id ? -1 : 0; + }); }); // load genomes diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/scripts/packed/mvc/upload/upload-extensions.js --- a/static/scripts/packed/mvc/upload/upload-extensions.js +++ /dev/null @@ -1,1 +0,0 @@ -define([],function(){var a={auto:{text:"The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed"},ab1:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Ab1",text:"A binary sequence file in 'ab1' format with a '.ab1' file extension. You must manually select this 'File Format' when uploading the file."},axt:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Axt",text:"blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields."},bam:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#BAM",text:"A binary file compressed in the BGZF format with a '.bam' file extension."},bed:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Bed",text:"BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required columns and nine additional optional columns. The three required columns are chrom, chromStart and chromEnd."},fasta:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Fasta",text:'A sequence in FASTA format consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. All lines should be shorter than 80 characters.'},fastq:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Fastq",text:"FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. "},fastqsolexa:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa",text:"FastqSolexa is the Illumina (Solexa) variant of the Fastq format, which stores sequences and quality scores in a single file."},gff:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#GFF",text:"GFF lines have nine required fields that must be tab-separated."},gff3:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#GFF3",text:"The GFF3 format addresses the most common extensions to GFF, while preserving backward compatibility with previous formats."},interval:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#GFF3",text:"File must start with definition line in the following format (columns may be in any order)."},lav:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#GFF3",text:"Lav is the primary output format for BLASTZ. The first line of a .lav file begins with #:lav.."},maf:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#MAF",text:'TBA and multiz multiple alignment format. The first line of a .maf file begins with ##maf. This word is followed by white-space-separated "variable=value" pairs. There should be no white space surrounding the "=".'},scf:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Scf",text:"A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file."},sff:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Sff",text:"A binary file in 'Standard Flowgram Format' with a '.sff' file extension."},tabular:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Tabular_.28tab_delimited.29",text:"Any data in tab delimited format (tabular)."},wig:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Wig",text:"The wiggle format is line-oriented. Wiggle data is preceded by a track definition line, which adds a number of options for controlling the default display of this track."},txt:{url:"https://wiki.galaxyproject.org/Learn/Datatypes#Plain_text",text:"Any text file."},};return function(c){var d=a[c];if(d){var b=d.text;if(d.url){b+=' (<a href="'+d.url+'" target="_blank">read more</a>)'}return b}else{return"There is no description available for this file extension."}}}); \ No newline at end of file diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/scripts/packed/mvc/upload/upload-row.js --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-extensions","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,f,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(j,h){this.app=j;var g=this;this.model=new b.Model(h);this.setElement(this._template(h));var i=this.$el;this.settings=new c.View({title:"Upload configuration",container:i.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){g.model.set("genome",g.select_genome.value())},data:g.app.list_genomes,container:i.find("#genome"),value:g.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){g.model.set("extension",g.select_extension.value())},data:g.app.list_extensions,container:i.find("#extension"),value:g.model.get("extension")});i.find("#symbol").on("click",function(){g._removeRow()});i.find("#extension-info").on("click",function(k){g._showExtensionInfo()}).on("mousedown",function(k){k.preventDefault()});i.find("#settings").on("click",function(k){g._showSettings()}).on("mousedown",function(k){k.preventDefault()});i.find("#text-content").on("keyup",function(k){g.model.set("url_paste",$(k.target).val());g.model.set("file_size",$(k.target).val().length)});i.find("#space_to_tabs").on("change",function(k){g.model.set("space_to_tabs",$(k.target).prop("checked"))});this.model.on("change:percentage",function(){g._refreshPercentage()});this.model.on("change:status",function(){g._refreshStatus()});this.model.on("change:info",function(){g._refreshInfo()});this.model.on("change:genome",function(){g._refreshGenome()});this.model.on("change:file_size",function(){g._refreshFileSize()});this.model.on("remove",function(){g.remove()});this.app.collection.on("reset",function(){g.remove()})},render:function(){var n=this.model.get("file_name");var h=this.model.get("file_size");var k=this.model.get("file_mode");var j=this.$el;j.find("#title").html(n);j.find("#size").html(d.bytesToString(h));j.find("#mode").removeClass().addClass("mode");if(k=="new"){var m=j.find("#text");var l=this.options.padding;var i=j.width()-2*l;var g=j.height()-l;m.css("width",i+"px");m.css("top",g+"px");j.height(g+m.height()+2*l);m.show();j.find("#mode").addClass("fa fa-pencil")}if(k=="local"){j.find("#mode").addClass("fa fa-laptop")}if(k=="ftp"){j.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var g=this.model.get("genome");this.select_genome.value(g)},_refreshInfo:function(){var g=this.model.get("info");if(g){this.$el.find("#info").html("<strong>Failed: </strong>"+g).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var g=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:g+"%"});if(g!=100){this.$el.find("#percentage").html(g+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var h=this.$el;var g=this.model.get("status");var j=this.status_classes[g];var i=this.$el.find("#symbol");i.removeClass();i.addClass(j);if(g=="init"){this.select_genome.enable();this.select_extension.enable();h.find("#text-content").attr("disabled",false);h.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();h.find("#text-content").attr("disabled",true);h.find("#space_to_tabs").attr("disabled",true)}if(g=="success"){h.addClass("success");h.find("#percentage").html("100%")}if(g=="error"){h.addClass("danger");h.find(".progress").remove()}},_refreshFileSize:function(){var g=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(g))},_removeRow:function(){var g=this.model.get("status");if(g=="init"||g=="success"||g=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var g=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();if(!this.extension_popup){this.extension_popup=new c.View({content:f(i),placement:"bottom",container:g})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(f(i));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_template:function(g){return'<tr id="upload-item-'+g.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file +define(["utils/utils","mvc/upload/upload-model","mvc/upload/upload-settings","mvc/ui/ui-popover","mvc/ui/ui-select"],function(d,b,a,c,e){return Backbone.View.extend({options:{padding:8},status_classes:{init:"upload-icon-button fa fa-trash-o",queued:"upload-icon fa fa-spinner fa-spin",running:"upload-icon fa fa-spinner fa-spin",success:"upload-icon-button fa fa-check",error:"upload-icon-button fa fa-exclamation-triangle"},settings:null,select_genome:null,select_extension:null,initialize:function(i,g){this.app=i;var f=this;this.model=new b.Model(g);this.setElement(this._template(g));var h=this.$el;this.settings=new c.View({title:"Upload configuration",container:h.find("#settings"),placement:"bottom"});this.select_genome=new e.View({css:"genome",onchange:function(){f.model.set("genome",f.select_genome.value())},data:f.app.list_genomes,container:h.find("#genome"),value:f.model.get("genome")});this.select_extension=new e.View({css:"extension",onchange:function(){f.model.set("extension",f.select_extension.value())},data:f.app.list_extensions,container:h.find("#extension"),value:f.model.get("extension")});h.find("#symbol").on("click",function(){f._removeRow()});h.find("#extension-info").on("click",function(j){f._showExtensionInfo()}).on("mousedown",function(j){j.preventDefault()});h.find("#settings").on("click",function(j){f._showSettings()}).on("mousedown",function(j){j.preventDefault()});h.find("#text-content").on("keyup",function(j){f.model.set("url_paste",$(j.target).val());f.model.set("file_size",$(j.target).val().length)});h.find("#space_to_tabs").on("change",function(j){f.model.set("space_to_tabs",$(j.target).prop("checked"))});this.model.on("change:percentage",function(){f._refreshPercentage()});this.model.on("change:status",function(){f._refreshStatus()});this.model.on("change:info",function(){f._refreshInfo()});this.model.on("change:genome",function(){f._refreshGenome()});this.model.on("change:file_size",function(){f._refreshFileSize()});this.model.on("remove",function(){f.remove()});this.app.collection.on("reset",function(){f.remove()})},render:function(){var m=this.model.get("file_name");var g=this.model.get("file_size");var j=this.model.get("file_mode");var i=this.$el;i.find("#title").html(m);i.find("#size").html(d.bytesToString(g));i.find("#mode").removeClass().addClass("mode");if(j=="new"){var l=i.find("#text");var k=this.options.padding;var h=i.width()-2*k;var f=i.height()-k;l.css("width",h+"px");l.css("top",f+"px");i.height(f+l.height()+2*k);l.show();i.find("#mode").addClass("fa fa-pencil")}if(j=="local"){i.find("#mode").addClass("fa fa-laptop")}if(j=="ftp"){i.find("#mode").addClass("fa fa-code-fork")}},remove:function(){this.select_genome.remove();this.select_extension.remove();Backbone.View.prototype.remove.apply(this)},_refreshGenome:function(){var f=this.model.get("genome");this.select_genome.value(f)},_refreshInfo:function(){var f=this.model.get("info");if(f){this.$el.find("#info").html("<strong>Failed: </strong>"+f).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var f=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:f+"%"});if(f!=100){this.$el.find("#percentage").html(f+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var g=this.$el;var f=this.model.get("status");var i=this.status_classes[f];var h=this.$el.find("#symbol");h.removeClass();h.addClass(i);if(f=="init"){this.select_genome.enable();this.select_extension.enable();g.find("#text-content").attr("disabled",false);g.find("#space_to_tabs").attr("disabled",false)}else{this.select_genome.disable();this.select_extension.disable();g.find("#text-content").attr("disabled",true);g.find("#space_to_tabs").attr("disabled",true)}if(f=="success"){g.addClass("success");g.find("#percentage").html("100%")}if(f=="error"){g.addClass("danger");g.find(".progress").remove()}},_refreshFileSize:function(){var f=this.model.get("file_size");this.$el.find("#size").html(d.bytesToString(f))},_removeRow:function(){var f=this.model.get("status");if(f=="init"||f=="success"||f=="error"){this.app.collection.remove(this.model)}},_showExtensionInfo:function(){var f=$(this.el).find("#extension-info");var i=this.model.get("extension");var h=this.select_extension.text();var g=d.findPair(this.app.list_extensions,"id",i);if(!this.extension_popup){this.extension_popup=new c.View({placement:"bottom",container:f})}if(!this.extension_popup.visible){this.extension_popup.title(h);this.extension_popup.empty();this.extension_popup.append(this._templateDescription(g));this.extension_popup.show()}else{this.extension_popup.hide()}},_showSettings:function(){if(!this.settings.visible){this.settings.empty();this.settings.append((new a(this)).$el);this.settings.show()}else{this.settings.hide()}},_templateDescription:function(g){if(g.description){var f=g.description;if(g.description_url){f+=' (<a href="'+g.description_url+'" target="_blank">read more</a>)'}return f}else{return"There is no description available for this file extension."}},_template:function(f){return'<tr id="upload-item-'+f.id+'" class="upload-item"><td><div style="position: relative;"><div id="mode"></div><div id="title" class="title"></div><div id="text" class="text"><div class="text-info">You can tell Galaxy to download data from web by entering URL in this box (one per line). You can also directly paste the contents of a file.</div><textarea id="text-content" class="text-content form-control"></textarea></div></div></td><td><div id="size" class="size"></div></td><td><div id="extension" class="extension" style="float: left;"/> &nbsp<div id="extension-info" class="upload-icon-button fa fa-search"/></td><td><div id="genome" class="genome" /></td><td><div id="settings" class="upload-icon-button fa fa-gear"></div><td><div id="info" class="info"><div class="progress"><div class="progress-bar progress-bar-success"></div><div id="percentage" class="percentage">0%</div></div></div></td><td><div id="symbol" class="'+this.status_classes.init+'"></div></td></tr>'}})}); \ No newline at end of file diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/scripts/packed/mvc/upload/upload-view.js --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect"}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?upload_only=True",function(j){for(key in j){h.list_extensions.push({id:j[key],text:j[key]})}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-button","mvc/upload/upload-model","mvc/upload/upload-row","mvc/upload/upload-ftp","mvc/ui/ui-popover","mvc/ui","utils/uploadbox"],function(a,f,e,c,b,g,d){return Backbone.View.extend({options:{nginx_upload_path:""},modal:null,ui_button:null,uploadbox:null,current_history:null,upload_size:0,list_extensions:[{id:"auto",text:"Auto-detect",description:"The system will attempt to detect Axt, Fasta, Fastqsolexa, Gff, Gff3, Html, Lav, Maf, Tabular, Wiggle, Bed and Interval (Bed with headers) formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."}],list_genomes:[],collection:new c.Collection(),ftp:null,counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel||!Galaxy.currHistoryPanel.model){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.ui_button=new e.Model({icon:"fa-upload",tooltip:"Download from URL or upload files from disk",label:"Load Data",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new e.View(this.ui_button)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes?extension_only=False",function(j){for(key in j){h.list_extensions.push({id:j[key].extension,text:j[key].extension,description:j[key].description,description_url:j[key].description_url})}h.list_extensions.sort(function(l,k){if(l.id=="auto"){return -1}if(k.id=="auto"){return 1}return l.id>k.id?1:l.id<k.id?-1:0})});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){for(key in j){h.list_genomes.push({id:j[key][1],text:j[key][0]})}h.list_genomes.sort(function(l,k){return l.id>k.id?1:l.id<k.id?-1:0})});if(i){this.options=_.defaults(i,this.options)}this.collection.on("remove",function(j){h._eventRemove(j)});this.collection.on("change:genome",function(k){var j=k.get("genome");h.collection.each(function(l){if(l.get("status")=="init"&&l.get("genome")=="?"){l.set("genome",j)}})})},_eventShow:function(j){j.preventDefault();if(!this.modal){var h=this;this.modal=new a.GalaxyModal({title:"Download data directly from web or upload files from your disk",body:this._template("upload-box","upload-info"),buttons:{"Choose local file":function(){h.uploadbox.select()},"Choose FTP file":function(){h._eventFtp()},"Create new file":function(){h._eventCreate()},Start:function(){h._eventStart()},Pause:function(){h._eventStop()},Reset:function(){h._eventReset()},Close:function(){h.modal.hide()},},height:"400",width:"900",closing_events:true});this.setElement("#upload-box");var h=this;this.uploadbox=this.$el.uploadbox({announce:function(k,l,m){h._eventAnnounce(k,l,m)},initialize:function(k,l,m){return h._eventInitialize(k,l,m)},progress:function(k,l,m){h._eventProgress(k,l,m)},success:function(k,l,m){h._eventSuccess(k,l,m)},error:function(k,l,m){h._eventError(k,l,m)},complete:function(){h._eventComplete()}});this._updateScreen();if(this.options.ftp_upload_dir&&this.options.ftp_upload_site){var i=this.modal.getButton("Choose FTP file");this.ftp=new d.View({title:"FTP files",container:i})}else{this.modal.hideButton("Choose FTP file")}}this.modal.show()},_eventRemove:function(i){var h=i.get("status");if(h=="success"){this.counter.success--}else{if(h=="error"){this.counter.error--}else{this.counter.announce--}}this._updateScreen();this.uploadbox.remove(i.id)},_eventAnnounce:function(h,i,k){this.counter.announce++;this._updateScreen();var j=new b(this,{id:h,file_name:i.name,file_size:i.size,file_mode:i.mode,file_path:i.path});this.collection.add(j.model);$(this.el).find("tbody:first").append(j.$el);j.render()},_eventInitialize:function(m,j,s){var k=this.collection.get(m);k.set("status","running");var o=k.get("file_name");var n=k.get("file_path");var h=k.get("file_mode");var p=k.get("extension");var r=k.get("genome");var q=k.get("url_paste");var l=k.get("space_to_tabs");var i=k.get("to_posix_lines");if(!q&&!(j.size>0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path});if(h=="local"){this.uploadbox.configure({paramname:"files_0|file_data"})}else{this.uploadbox.configure({paramname:null})}tool_input={};if(h=="new"){tool_input["files_0|url_paste"]=q}if(h=="ftp"){tool_input["files_0|ftp_files"]=n}tool_input.dbkey=r;tool_input.file_type=p;tool_input["files_0|type"]="upload_dataset";tool_input.space_to_tabs=l;tool_input.to_posix_lines=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.ui_button.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("percentage",100);k.set("status","success");var h=k.get("file_size");this.ui_button.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("percentage",100);j.set("status","error");j.set("info",k);this.ui_button.set("percentage",this._upload_percentage(100,i.size));this.ui_button.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventFtp:function(){if(!this.ftp.visible){this.ftp.empty();this.ftp.append((new g(this)).$el);this.ftp.show()}else{this.ftp.hide()}},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:0,mode:"new"}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.ui_button.set("percentage",0);this.ui_button.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.ui_button.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.ui_button.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="You can Drag & Drop files into this box."}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Some supported browsers are: Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Start' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Start")}else{this.modal.disableButton("Start")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Choose local file");this.modal.enableButton("Choose FTP file");this.modal.enableButton("Create new file")}else{this.modal.disableButton("Choose local file");this.modal.disableButton("Choose FTP file");this.modal.disableButton("Create new file")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("#upload-table").show()}else{$(this.el).find("#upload-table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'<div id="'+i+'" class="upload-box"><table id="upload-table" class="table table-striped" style="display: none;"><thead><tr><th>Name</th><th>Size</th><th>Type</th><th>Genome</th><th>Settings</th><th>Status</th><th></th></tr></thead><tbody></tbody></table></div><h6 id="'+h+'" class="upload-info"></h6>'}})}); \ No newline at end of file diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/scripts/packed/utils/utils.js --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(c){function f(j,i,h){var k=new XMLHttpRequest();k.open("GET",j,true);k.setRequestHeader("Accept","application/json");k.setRequestHeader("Cache-Control","no-cache");k.setRequestHeader("X-Requested-With","XMLHttpRequest");k.onloadend=function(){var l=k.status;if(l==200){try{response=jQuery.parseJSON(k.responseText)}catch(m){response=k.responseText}i&&i(response)}else{h&&h(l)}};k.send()}function b(k,h){var i=$('<div class="'+k+'"></div>');i.appendTo(":eq(0)");var j=i.css(h);i.remove();return j}function a(h){if(!$('link[href^="'+h+'"]').length){$('<link href="'+galaxy_config.root+h+'" rel="stylesheet">').appendTo("head")}}function g(h,i){if(h){return c.defaults(h,i)}else{return i}}function d(i,k){var j="";if(i>=100000000000){i=i/100000000000;j="TB"}else{if(i>=100000000){i=i/100000000;j="GB"}else{if(i>=100000){i=i/100000;j="MB"}else{if(i>=100){i=i/100;j="KB"}else{if(i>0){i=i*10;j="b"}else{return"<strong>-</strong>"}}}}}var h=(Math.round(i)/10);if(k){return h+" "+j}else{return"<strong>"+h+"</strong> "+j}}function e(){return(new Date().getTime()).toString(36)}return{cssLoadFile:a,cssGetAttribute:b,jsonFromUrl:f,merge:g,bytesToString:d,uuid:e}}); \ No newline at end of file +define(["libs/underscore"],function(c){function f(k,j,i){var l=new XMLHttpRequest();l.open("GET",k,true);l.setRequestHeader("Accept","application/json");l.setRequestHeader("Cache-Control","no-cache");l.setRequestHeader("X-Requested-With","XMLHttpRequest");l.onloadend=function(){var m=l.status;if(m==200){try{response=jQuery.parseJSON(l.responseText)}catch(n){response=l.responseText}j&&j(response)}else{i&&i(m)}};l.send()}function b(l,i){var j=$('<div class="'+l+'"></div>');j.appendTo(":eq(0)");var k=j.css(i);j.remove();return k}function a(i){if(!$('link[href^="'+i+'"]').length){$('<link href="'+galaxy_config.root+i+'" rel="stylesheet">').appendTo("head")}}function h(i,j){if(i){return c.defaults(i,j)}else{return j}}function d(j,l){var k="";if(j>=100000000000){j=j/100000000000;k="TB"}else{if(j>=100000000){j=j/100000000;k="GB"}else{if(j>=100000){j=j/100000;k="MB"}else{if(j>=100){j=j/100;k="KB"}else{if(j>0){j=j*10;k="b"}else{return"<strong>-</strong>"}}}}}var i=(Math.round(j)/10);if(l){return i+" "+k}else{return"<strong>"+i+"</strong> "+k}}function e(){return(new Date().getTime()).toString(36)}function g(j,l,n){for(var k in j){var m=j[k];if(m[l]==n){return m}}return{}}return{cssLoadFile:a,cssGetAttribute:b,jsonFromUrl:f,merge:h,bytesToString:d,uuid:e,findPair:g}}); \ No newline at end of file diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/scripts/utils/utils.js --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -96,6 +96,17 @@ return (new Date().getTime()).toString(36); }; +// find in dict +function findPair(arr, key, val) { + for (var i in arr) { + var item = arr[i]; + if (item[key] == val) { + return item; + } + } + return {}; +} + // return return { cssLoadFile : cssLoadFile, @@ -103,7 +114,8 @@ jsonFromUrl : jsonFromUrl, merge : merge, bytesToString: bytesToString, - uuid: uuid + uuid: uuid, + findPair: findPair }; }); diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1261,7 +1261,7 @@ .upload-info{font-weight:normal;text-align:center} .upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%} .upload-box .table th{text-align:center;white-space:nowrap} -.upload-box .table td{margin:0px;paddign:0px} +.upload-box .table td{margin:0px} .upload-box .upload-item .select2-arrow b{background-position:0 -3px} .upload-box .upload-item .select2-choice{max-height:20px;line-height:18px;background:transparent} .upload-box .upload-item .select2-container-disabled .select2-arrow{background:transparent} diff -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d -r 72eec07ef71833f797c7e279a6c27c4e8a24535c static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -82,7 +82,6 @@ .table td { margin: 0px; - paddign: 0px; } .upload-item { 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 14 Feb '14

14 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fa8bdf1f6fc7/ Changeset: fa8bdf1f6fc7 Branch: stable User: inithello Date: 2014-02-14 21:59:35 Summary: Also check for tool config path when installing migrated tools and rewriting the tool_conf.xml. This resolves the issue described in pull request 324. Affected #: 1 file diff -r 75672e1cba2bd569b729156f3d8f8f1f994240f0 -r fa8bdf1f6fc7318d120a3420c50e4045dbdb1e8b lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -197,8 +197,7 @@ file_path = section_elem.get( 'file', None ) if file_path: file_name = suc.strip_path( file_path ) - - if file_name in tool_configs_to_filter: + if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter: elem.remove( section_elem ) persist_required = True if persist_required: @@ -223,7 +222,7 @@ # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: + if tool_config == proprietary_name or tool_config == proprietary_tool_config: # The tool is loaded outside of any sections. tool_sections.append( None ) if not is_displayed: @@ -235,7 +234,7 @@ # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = section_elem.get( 'file' ) proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: + if tool_config == proprietary_name or tool_config == proprietary_tool_config: # The tool is loaded inside of the section_elem. tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) if not is_displayed: @@ -314,7 +313,7 @@ file_path = elem.get( 'file', None ) if file_path: name = suc.strip_path( file_path ) - if name in migrated_tool_configs: + if name in migrated_tool_configs or file_path in migrated_tool_configs: if elem not in tool_panel_elems: tool_panel_elems.append( elem ) elif elem.tag == 'section': @@ -324,7 +323,7 @@ file_path = section_elem.get( 'file', None ) if file_path: name = suc.strip_path( file_path ) - if name in migrated_tool_configs: + if name in migrated_tool_configs or file_path in migrated_tool_configs: # Append the section, not the tool. if elem not in tool_panel_elems: tool_panel_elems.append( elem ) https://bitbucket.org/galaxy/galaxy-central/commits/5079dae08441/ Changeset: 5079dae08441 User: inithello Date: 2014-02-14 22:00:00 Summary: Merge bugfix from stable. Affected #: 1 file diff -r 479b72075bc8a68ec602081987375ca1dfa20a2f -r 5079dae08441dcf125cc9fee87b28aaba7a38f9d lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -197,8 +197,7 @@ file_path = section_elem.get( 'file', None ) if file_path: file_name = suc.strip_path( file_path ) - - if file_name in tool_configs_to_filter: + if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter: elem.remove( section_elem ) persist_required = True if persist_required: @@ -223,7 +222,7 @@ # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: + if tool_config == proprietary_name or tool_config == proprietary_tool_config: # The tool is loaded outside of any sections. tool_sections.append( None ) if not is_displayed: @@ -235,7 +234,7 @@ # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = section_elem.get( 'file' ) proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name: + if tool_config == proprietary_name or tool_config == proprietary_tool_config: # The tool is loaded inside of the section_elem. tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) if not is_displayed: @@ -314,7 +313,7 @@ file_path = elem.get( 'file', None ) if file_path: name = suc.strip_path( file_path ) - if name in migrated_tool_configs: + if name in migrated_tool_configs or file_path in migrated_tool_configs: if elem not in tool_panel_elems: tool_panel_elems.append( elem ) elif elem.tag == 'section': @@ -324,7 +323,7 @@ file_path = section_elem.get( 'file', None ) if file_path: name = suc.strip_path( file_path ) - if name in migrated_tool_configs: + if name in migrated_tool_configs or file_path in migrated_tool_configs: # Append the section, not the tool. if elem not in tool_panel_elems: tool_panel_elems.append( elem ) 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.

1 0

commit/galaxy-central: carlfeberhard: Scatterplot: small style fixes
by commits-noreply＠bitbucket.org 14 Feb '14

14 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/479b72075bc8/ Changeset: 479b72075bc8 User: carlfeberhard Date: 2014-02-14 21:34:27 Summary: Scatterplot: small style fixes Affected #: 5 files diff -r 8494c2b3a3edff7f900a9994ccd806d063d5010f -r 479b72075bc8a68ec602081987375ca1dfa20a2f config/plugins/visualizations/scatterplot/src/scatterplot-display.js --- a/config/plugins/visualizations/scatterplot/src/scatterplot-display.js +++ b/config/plugins/visualizations/scatterplot/src/scatterplot-display.js @@ -53,14 +53,14 @@ template : function(){ var html = [ '<div class="controls clear">', - '<div class="left">', - '<div class="page-control"></div>', - '</div>', '<div class="right">', '<p class="scatterplot-data-info"></p>', '<button class="stats-toggle-btn">Stats</button>', '<button class="rerender-btn">Redraw</button>', '</div>', + '<div class="left">', + '<div class="page-control"></div>', + '</div>', '</div>', '<svg/>', //TODO: id '<div class="stats-display"></div>' diff -r 8494c2b3a3edff7f900a9994ccd806d063d5010f -r 479b72075bc8a68ec602081987375ca1dfa20a2f config/plugins/visualizations/scatterplot/static/scatterplot-edit.js --- a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js +++ b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js @@ -1,1 +1,1 @@ -function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.x.ticks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.y.ticks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("class","axis-label").text(b.x.label).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("class","axis-label").text(b.y.label).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="'+i((f=b.x,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+i((f=b.y,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){function f(a,b){var d,e="";return e+='\n <option value="',(d=c.index)?d=d.call(a,{hash:{},data:b}):(d=a.index,d=typeof d===j?d.apply(a):d),e+=k(d)+'">',(d=c.name)?d=d.call(a,{hash:{},data:b}):(d=a.name,d=typeof d===j?d.apply(a):d),e+=k(d)+"</option>\n "}function g(){return'checked="true"'}this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var h,i="",j="function",k=this.escapeExpression,l=this;return i+='<p class="help-text">\n Use the following controls to change the data used by the chart.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n\n<div class="column-select">\n <label>Data column for X: </label>\n <select name="xColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n<div class="column-select">\n <label>Data column for Y: </label>\n <select name="yColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n</div>\n<div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="idColumn">\n ',h=c.each.call(b,b.allColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="first-line-header" style="display: none;">\n <p>Possible headers: ',(h=c.possibleHeaders)?h=h.call(b,{hash:{},data:e}):(h=b.possibleHeaders,h=typeof h===j?h.apply(b):h),i+=k(h)+'\n </p>\n <label for="first-line-header-checkbox">Use the above as column headers?</label>\n <input type="checkbox" name="include-id" id="first-line-header-checkbox"\n ',h=c["if"].call(b,b.usePossibleHeaders,{hash:{},inverse:l.noop,fn:l.program(3,g,e),data:e}),(h||0===h)&&(i+=h),i+='/>\n <p class="help-text-small">\n It looks like Galaxy couldn\'t get proper column headers for this data.\n Would you like to use the column headers above as column names to select columns?\n </p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div id="data-control" class="scatterplot-config-control tab-pane active">\n \n </div>\n \n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n \n </div>\n\n \n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'});var ScatterplotConfigEditor=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),this.log(this+".initialize, attributes:",a),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.log("dataset:",this.dataset),this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.dataset,d=c.metadata_column_names||[],e=this.model.get("config"),f=[],g=_.map(c.metadata_column_types,function(a,b){var c={index:b,type:a,name:d[b]||"column "+(b+1)};return("int"===c.type||"float"===c.type)&&f.push(c),c});f.length<2&&(f=g);var h=a.find(".tab-pane#data-control");h.html(ScatterplotConfigEditor.templates.dataControl({allColumns:g,numericColumns:f}));var i={xColumn:_.isFinite(e.xColumn)?e.xColumn:f[0].index,yColumn:_.isFinite(e.yColumn)?e.yColumn:f[1].index,idColumn:g[0].index};if(_.isFinite(e.idColumn))i.idColumn=e.idColumn;else if(g.length>2){var j=_.find(g,function(a,b){return b!==i.xColumn&&b!==i.yColumn});i.idColumn=j.index}return e=this.model.set("config",i,{silent:!0}).get("config"),h.find('[name="xColumn"]').val(e.xColumn).on("change",function(){b.model.set("config",{xColumn:Number($(this).val())})}),h.find('[name="yColumn"]').val(e.yColumn).on("change",function(){b.model.set("config",{yColumn:Number($(this).val())})}),h.find('select[name="idColumn"]').val(e.idColumn).on("change",function(){b.model.set("config",{idColumn:Number($(this).val())})}),void 0!==e.idColumn&&h.find("#include-id-checkbox").prop("checked",!0).trigger("change"),h.find("[title]").tooltip(),h},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="left">','<div class="page-control"></div>',"</div>",'<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.x.label,e=b.y.label,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}}); \ No newline at end of file +function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){$(".chart-info-box").remove(),q.redraw(),e(),s=d(),$(o.node()).trigger("zoom.scatterplot",{scale:n.scale(),translate:n.translate()})}function g(a,c,d){return c+=8,$(['<div class="chart-info-box" style="position: absolute">',void 0!==b.idColumn?"<div>"+d[b.idColumn]+"</div>":"","<div>",j(d),"</div>","<div>",k(d),"</div>","</div>"].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,30]).scale(b.scale||1).translate(b.translate||[0,0]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.x.ticks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.y.ticks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=6;q.x.label=o.append("text").attr("class","axis-label").text(b.x.label).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("class","axis-label").text(b.y.label).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",0);t.transition().duration(b.animDuration).attr("r",b.datapointSize),e(),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.classed("highlight",!0).style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")<b.height&&p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")).attr("y1",+d.attr("cy")+b.datapointSize).attr("x2",d.attr("cx")).attr("y2",b.height).classed("hoverline",!0);var e=this.getBoundingClientRect();$("body").append(g(e.top,e.right,a)),$(o.node()).trigger("mouseover-datapoint.scatterplot",[this,a,c])}),t.on("mouseout",function(){d3.select(this).classed("highlight",!1).style("fill","black").style("fill-opacity",.2),p.selectAll(".hoverline").remove(),$(".chart-info-box").remove()})}this.scatterplot=this.scatterplot||{},this.scatterplot.chartcontrol=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='<p class="help-text">\n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n<div data-config-key="datapointSize" class="form-input numeric-slider-input">\n <label for="datapointSize">Size of data point: </label>\n <div class="slider-output">',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n Size of the graphic representation of each data point\n </p>\n</div>\n\n<div data-config-key="width" class="form-input numeric-slider-input">\n <label for="width">Chart width: </label>\n <div class="slider-output">',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="height" class="form-input numeric-slider-input">\n <label for="height">Chart height: </label>\n <div class="slider-output">',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'</div>\n <div class="slider"></div>\n <p class="form-help help-text-small">\n (not including chart margins and axes)\n </p>\n</div>\n\n<div data-config-key="X-axis-label"class="text-input form-input">\n <label for="X-axis-label">Re-label the X axis: </label>\n <input type="text" name="X-axis-label" id="X-axis-label" value="'+i((f=b.x,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<div data-config-key="Y-axis-label" class="text-input form-input">\n <label for="Y-axis-label">Re-label the Y axis: </label>\n <input type="text" name="Y-axis-label" id="Y-axis-label" value="'+i((f=b.y,f=null==f||f===!1?f:f.label,typeof f===h?f.apply(b):f))+'" />\n <p class="form-help help-text-small"></p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){function f(a,b){var d,e="";return e+='\n <option value="',(d=c.index)?d=d.call(a,{hash:{},data:b}):(d=a.index,d=typeof d===j?d.apply(a):d),e+=k(d)+'">',(d=c.name)?d=d.call(a,{hash:{},data:b}):(d=a.name,d=typeof d===j?d.apply(a):d),e+=k(d)+"</option>\n "}function g(){return'checked="true"'}this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var h,i="",j="function",k=this.escapeExpression,l=this;return i+='<p class="help-text">\n Use the following controls to change the data used by the chart.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n</p>\n\n\n<div class="column-select">\n <label>Data column for X: </label>\n <select name="xColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n<div class="column-select">\n <label>Data column for Y: </label>\n <select name="yColumn">\n ',h=c.each.call(b,b.numericColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="include-id">\n <label for="include-id-checkbox">Include a third column as data point IDs?</label>\n <input type="checkbox" name="include-id" id="include-id-checkbox" />\n <p class="help-text-small">\n These will be displayed (along with the x and y values) when you hover over\n a data point.\n </p>\n</div>\n<div class="column-select" style="display: none">\n <label for="ID-select">Data column for IDs: </label>\n <select name="idColumn">\n ',h=c.each.call(b,b.allColumns,{hash:{},inverse:l.noop,fn:l.program(1,f,e),data:e}),(h||0===h)&&(i+=h),i+='\n </select>\n</div>\n\n\n<div id="first-line-header" style="display: none;">\n <p>Possible headers: ',(h=c.possibleHeaders)?h=h.call(b,{hash:{},data:e}):(h=b.possibleHeaders,h=typeof h===j?h.apply(b):h),i+=k(h)+'\n </p>\n <label for="first-line-header-checkbox">Use the above as column headers?</label>\n <input type="checkbox" name="include-id" id="first-line-header-checkbox"\n ',h=c["if"].call(b,b.usePossibleHeaders,{hash:{},inverse:l.noop,fn:l.program(3,g,e),data:e}),(h||0===h)&&(i+=h),i+='/>\n <p class="help-text-small">\n It looks like Galaxy couldn\'t get proper column headers for this data.\n Would you like to use the column headers above as column names to select columns?\n </p>\n</div>\n\n<button class="render-button btn btn-primary active">Draw</button>\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='<div class="scatterplot-editor tabbable tabs-left">\n \n <ul class="nav nav-tabs">\n \n <li class="active">\n <a title="Use this tab to change which data are used"\n href="#data-control" data-toggle="tab">Data Controls</a>\n </li>\n <li>\n <a title="Use this tab to change how the chart is drawn"\n href="#chart-control" data-toggle="tab" >Chart Controls</a>\n </li>\n \n <li class="disabled">\n <a title="This tab will display the chart"\n href="#chart-display" data-toggle="tab">Chart</a>\n </li>\n \n <li class="file-controls">\n\n <button class="save-btn btn btn-default">Save</button>\n </li>\n </ul>\n\n \n <div class="tab-content">\n \n <div id="data-control" class="scatterplot-config-control tab-pane active">\n \n </div>\n \n \n <div id="chart-control" class="scatterplot-config-control tab-pane">\n \n </div>\n\n \n <div id="chart-display" class="scatterplot-display tab-pane"></div>\n\n </div>\n</div>\n'});var ScatterplotConfigEditor=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),this.log(this+".initialize, attributes:",a),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,this.log("dataset:",this.dataset),this.display=new ScatterplotDisplay({dataset:a.dataset,model:this.model})},render:function(){this.$el.empty().append(ScatterplotConfigEditor.templates.mainLayout({})),this.model.id&&(this.$el.find(".copy-btn").show(),this.$el.find(".save-btn").text("Update saved")),this.$el.find("[title]").tooltip(),this._render_dataControl(),this._render_chartControls(),this._render_chartDisplay();var a=this.model.get("config");return this.model.id&&_.isFinite(a.xColumn)&&_.isFinite(a.yColumn)&&this.renderChart(),this},_render_dataControl:function(a){a=a||this.$el;var b=this,c=this.dataset,d=c.metadata_column_names||[],e=this.model.get("config"),f=[],g=_.map(c.metadata_column_types,function(a,b){var c={index:b,type:a,name:d[b]||"column "+(b+1)};return("int"===c.type||"float"===c.type)&&f.push(c),c});f.length<2&&(f=g);var h=a.find(".tab-pane#data-control");h.html(ScatterplotConfigEditor.templates.dataControl({allColumns:g,numericColumns:f}));var i={xColumn:_.isFinite(e.xColumn)?e.xColumn:f[0].index,yColumn:_.isFinite(e.yColumn)?e.yColumn:f[1].index,idColumn:g[0].index};if(_.isFinite(e.idColumn))i.idColumn=e.idColumn;else if(g.length>2){var j=_.find(g,function(a,b){return b!==i.xColumn&&b!==i.yColumn});i.idColumn=j.index}return e=this.model.set("config",i,{silent:!0}).get("config"),h.find('[name="xColumn"]').val(e.xColumn).on("change",function(){b.model.set("config",{xColumn:Number($(this).val())})}),h.find('[name="yColumn"]').val(e.yColumn).on("change",function(){b.model.set("config",{yColumn:Number($(this).val())})}),h.find('select[name="idColumn"]').val(e.idColumn).on("change",function(){b.model.set("config",{idColumn:Number($(this).val())})}),void 0!==e.idColumn&&h.find("#include-id-checkbox").prop("checked",!0).trigger("change"),h.find("[title]").tooltip(),h},_render_chartControls:function(a){function b(){var a=$(this),b=a.slider("value");c.model.set("config",_.object([[a.parent().data("config-key"),b]])),a.siblings(".slider-output").text(b)}a=a||this.$el;var c=this,d=this.model.get("config"),e=a.find("#chart-control");e.html(ScatterplotConfigEditor.templates.chartControl(d));var f={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};e.find(".numeric-slider-input").each(function(){var a=$(this),c=a.attr("data-config-key"),e=_.extend(f[c],{value:d[c],change:b,slide:b});a.find(".slider").slider(e),a.children(".slider-output").text(d[c])});var g=this.dataset.metadata_column_names||[],h=d.xLabel||g[d.xColumn]||"X",i=d.yLabel||g[d.yColumn]||"Y";return e.find('input[name="X-axis-label"]').val(h).on("change",function(){c.model.set("config",{xLabel:$(this).val()})}),e.find('input[name="Y-axis-label"]').val(i).on("change",function(){c.model.set("config",{yLabel:$(this).val()})}),e.find("[title]").tooltip(),e},_render_chartDisplay:function(a){a=a||this.$el;var b=a.find(".tab-pane#chart-display");return this.display.setElement(b),this.display.render(),b.find("[title]").tooltip(),b},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart","click .save-btn":"saveVisualization"},saveVisualization:function(){var a=this;this.model.save().fail(function(b,c,d){console.error(b,c,d),a.trigger("save:error",view),alert("Error loading data:\n"+b.responseText)}).then(function(){a.display.render()})},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.display.fetchData()},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotDisplay=Backbone.View.extend({initialize:function(a){this.data=null,this.dataset=a.dataset,this.lineCount=this.dataset.metadata_data_lines||null},fetchData:function(){this.showLoadingIndicator();var a=this,b=this.model.get("config"),c=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:b.pagination.perPage,offset:b.pagination.currPage*b.pagination.perPage});return c.done(function(b){a.data=b.data,a.trigger("data:fetched",a),a.renderData()}),c.fail(function(b,c,d){console.error(b,c,d),a.trigger("data:error",a),alert("Error loading data:\n"+b.responseText)}),c},showLoadingIndicator:function(){this.$el.find(".scatterplot-data-info").html(['<div class="loading-indicator">','<span class="fa fa-spinner fa-spin"></span>','<span class="loading-indicator-message">loading...</span>',"</div>"].join(""))},template:function(){var a=['<div class="controls clear">','<div class="right">','<p class="scatterplot-data-info"></p>','<button class="stats-toggle-btn">Stats</button>','<button class="rerender-btn">Redraw</button>',"</div>",'<div class="left">','<div class="page-control"></div>',"</div>","</div>","<svg/>",'<div class="stats-display"></div>'].join("");return a},render:function(){return this.$el.addClass("scatterplot-display").html(this.template()),this.data&&this.renderData(),this},renderData:function(){this.renderLeftControls(),this.renderRightControls(),this.renderPlot(this.data),this.getStats()},renderLeftControls:function(){var a=this,b=this.model.get("config");return this.$el.find(".controls .left .page-control").pagination({startingPage:b.pagination.currPage,perPage:b.pagination.perPage,totalDataSize:this.lineCount,currDataSize:this.data.length}).off().on("pagination.page-change",function(c,d){b.pagination.currPage=d,a.model.set("config",{pagination:b.pagination}),a.resetZoom(),a.fetchData()}),this},renderRightControls:function(){var a=this;this.setLineInfo(this.data),this.$el.find(".stats-toggle-btn").off().click(function(){a.toggleStats()}),this.$el.find(".rerender-btn").off().click(function(){a.resetZoom(),a.renderPlot(this.data)})},renderPlot:function(){var a=this,b=this.$el.find("svg");this.toggleStats(!1),b.off().empty().show().on("zoom.scatterplot",function(b,c){a.model.set("config",c)}),scatterplot(b.get(0),this.model.get("config"),this.data)},setLineInfo:function(a,b){if(a){var c=this.model.get("config"),d=this.lineCount||"an unknown total",e=c.pagination.currPage*c.pagination.perPage,f=e+a.length;this.$el.find(".controls p.scatterplot-data-info").text([e+1,"to",f,"of",d].join(" "))}else this.$el.find(".controls p.scatterplot-data-info").html(b||"");return this},resetZoom:function(a,b){return a=void 0!==a?a:1,b=void 0!==b?b:[0,0],this.model.set("config",{scale:a,translate:b}),this},getStats:function(){if(this.data){var a=this,b=this.model.get("config"),c=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js");c.postMessage({data:this.data,keys:[b.xColumn,b.yColumn]}),c.onerror=function(){c.terminate()},c.onmessage=function(b){a.renderStats(b.data)}}},renderStats:function(a){var b=this.model.get("config"),c=this.$el.find(".stats-display"),d=b.x.label,e=b.y.label,f=$("<table/>").addClass("table").append(["<thead><th></th><th>",d,"</th><th>",e,"</th></thead>"].join("")).append(_.map(a,function(a,b){return $(["<tr><td>",b,"</td><td>",a[0],"</td><td>",a[1],"</td></tr>"].join(""))}));c.empty().append(f)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500,scale:1,translate:[0,0]}}}); \ No newline at end of file diff -r 8494c2b3a3edff7f900a9994ccd806d063d5010f -r 479b72075bc8a68ec602081987375ca1dfa20a2f config/plugins/visualizations/scatterplot/static/scatterplot.css --- a/config/plugins/visualizations/scatterplot/static/scatterplot.css +++ b/config/plugins/visualizations/scatterplot/static/scatterplot.css @@ -1,8 +1,6 @@ * { margin: 0; padding: 0; } /* -------------------------------------------- header */ -.chart-header > * { margin: 0; padding: 0; } - .chart-header { margin-bottom: 16px; overflow: auto; @@ -40,7 +38,7 @@ /* -------------------------------------------- main layout */ .scatterplot-editor > * { margin: 0; padding: 0; } .scatterplot-editor .tab-pane { - padding: 8px; + padding-top: 8px; } .scatterplot-editor .help-text, @@ -134,6 +132,7 @@ border: 1px solid lightgrey; border-radius: 3px; padding: 8px 8px 4px 8px; + overflow: auto; } .scatterplot-display .controls button { @@ -144,25 +143,16 @@ } .scatterplot-display .pagination-scroll-container { - /* float left makes this not collapse very well */ - max-width: 540px; -} - -.scatterplot-display .controls .data-prev-next { + max-width: 440px; display: inline-block; - margin: 0px 4px 0px 0px; -} - -.scatterplot-display .controls { -} - -.scatterplot-display .controls .left, -.scatterplot-display .controls .right { - position: relative; } .scatterplot-display .controls .left { - float: left; + /*no shrinkwrap, but collapses well (with scroll)*/ + /*display: inline;*/ + /*will shrinkwrap*/ + display: inline-block; + /*display: table-cell;*/ } .scatterplot-display .controls .right { @@ -186,10 +176,13 @@ margin-left: 4px; } + /* -------------------------------------------- chart area */ svg.scatterplot { border: 1px solid lightgrey; border-radius: 3px; + /* doesn't work */ + overflow: auto; } svg.scatterplot .grid-line { diff -r 8494c2b3a3edff7f900a9994ccd806d063d5010f -r 479b72075bc8a68ec602081987375ca1dfa20a2f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1391,7 +1391,7 @@ .quota-meter-bar-error{background-color:#b93e3a} .quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000;white-space:nowrap} .pagination{margin:0px} -.pagination-scroll-container{overflow:auto;background-color:#F8F8F8;border-radius:3px;border:1px solid #BFBFBF} +.pagination-scroll-container{display:inline-block;background-color:#F8F8F8;border-radius:3px;border:1px solid #BFBFBF;overflow:auto} .pagination-scroll-container .pagination-page-list{margin:3px 0px 3px 0px} .pagination-scroll-container .pagination-page-list>li:first-child>a,.pagination-scroll-container .pagination-page-list>li:first-child>span{border-radius:0px;border-left:0px} .pagination-scroll-container .pagination-page-list>li:last-child>a,.pagination-scroll-container .pagination-page-list>li:last-child>span{border-radius:0px} diff -r 8494c2b3a3edff7f900a9994ccd806d063d5010f -r 479b72075bc8a68ec602081987375ca1dfa20a2f static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -514,10 +514,11 @@ } .pagination-scroll-container { - overflow : auto; + display : inline-block; background-color: #F8F8F8; border-radius : 3px; border : 1px solid #BFBFBF; + overflow : auto; } .pagination-scroll-container .pagination-page-list { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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