November 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: inithello: Added tool shed functional test features for tool metadata.
by Bitbucket 21 Nov '12

21 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1d078ed70cb8/ changeset: 1d078ed70cb8 user: inithello date: 2012-11-21 22:32:17 summary: Added tool shed functional test features for tool metadata. affected #: 2 files diff -r 7d278a17747ad9cb35b1af5ec011e46f814c339a -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -30,6 +30,11 @@ if strings_not_displayed: for string in strings_not_displayed: self.check_string_not_in_page( string ) + def check_for_tool_metadata(self, repository, changeset_revision, tool_id, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository/view_tool_metadata?repository_id=%s&changeset_revision=%s&tool_id=%s' % \ + ( self.security.encode_id( repository.id ), changeset_revision, tool_id ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def check_for_valid_tools( self, repository ): self.manage_repository( repository ) self.check_page_for_string( '<b>Valid tools</b><i> - click the name to preview the tool' ) @@ -118,6 +123,14 @@ tc.fv( "3", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def load_display_tool_page( self, repository, tool_xml_filename, changeset_revision, strings_displayed=[], strings_not_displayed=[] ): + repository_id = self.security.encode_id( repository.id ) + repo_subdirectory = '%03d' % int( repository.id / 1000 ) + tool_xml_path = '%2f'.join( [ 'database', 'community_files', repo_subdirectory, 'repo_%d' % repository.id, tool_xml_filename ] ) + url = '/repository/display_tool?repository_id=%s&tool_config=%s&changeset_revision=%s' % \ + ( repository_id, tool_xml_path, changeset_revision ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) def manage_repository( self, repository, strings_displayed=[], strings_not_displayed=[] ): url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) self.visit_url( url ) diff -r 7d278a17747ad9cb35b1af5ec011e46f814c339a -r 1d078ed70cb8faf207c6367761a683bf6d9c3e68 test/tool_shed/functional/test_0000_create_repository.py --- a/test/tool_shed/functional/test_0000_create_repository.py +++ b/test/tool_shed/functional/test_0000_create_repository.py @@ -69,11 +69,18 @@ strings_displayed=[ "The file '%s' has been successfully uploaded to the repository." % filter_filename ], \ commit_message="Uploaded filtering 1.1.0" ) self.check_for_valid_tools( repository ) - latest_changeset_revision = self.get_latest_repository_metadata_for_repository( repository ) + latest_repository_metadata = self.get_latest_repository_metadata_for_repository( repository ) + changeset_revision = latest_repository_metadata.changeset_revision self.check_repository_changelog( repository, strings_displayed=[ 'Repository metadata is associated with this change set.' ] ) self.set_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) self.unset_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) -# self.check_tool_metadata( repository, latest_changeset_revision, strings_displayed=[ 'Filter1' ] ) + self.load_display_tool_page( repository, tool_xml_filename='filtering.xml', \ + changeset_revision=changeset_revision, \ + strings_displayed=[ 'Filter (version 1.1.0)', "c1=='chr1'" ], \ + strings_not_displayed=[] ) + tool = latest_repository_metadata.metadata[ 'tools' ][0] + metadata_strings_displayed = [ tool[ 'guid' ], tool[ 'version' ], tool[ 'id' ], tool[ 'name' ], tool[ 'description' ], changeset_revision ] + self.check_for_tool_metadata( repository, changeset_revision, 'Filter1', strings_displayed=metadata_strings_displayed ) def test_0035_repository_browse_page( self ): '''Visit the repository browse page''' repository = get_repository_by_name( repository_name, admin_username ) 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: history panel: documenting fix to show display and edit attributes buttons for HDA in the error state.
by Bitbucket 21 Nov '12

21 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7d278a17747a/ changeset: 7d278a17747a user: carlfeberhard date: 2012-11-21 20:02:58 summary: history panel: documenting fix to show display and edit attributes buttons for HDA in the error state. affected #: 2 files diff -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 -r 7d278a17747ad9cb35b1af5ec011e46f814c339a static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -181,7 +181,8 @@ * @returns {jQuery} rendered DOM */ _render_displayButton : function(){ - // don't show display if not in ready state, error'd, or not accessible + // don't show display if not in ready state or not accessible + // DO show if in error (ala previous history panel) if( ( !this.model.inReadyState() ) //|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) diff -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 -r 7d278a17747ad9cb35b1af5ec011e46f814c339a static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -64,8 +64,8 @@ * @returns {jQuery} rendered DOM */ _render_editButton : function(){ - // don't show edit while uploading - //TODO??: error? + // don't show edit while uploading, in-accessible + // DO show if in error (ala previous history panel) //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ) //|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) 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: history panel: moved refresh into 'History' header bar. Moved 'Collapse Expanded Datasets', 'Show/Hide Deleted Datasets', and 'Show/Hide Hidden Datasets' into 'History' gear menu. Removed gear menu from current history. Packed scripts.
by Bitbucket 21 Nov '12

21 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8481560e2c32/ changeset: 8481560e2c32 user: carlfeberhard date: 2012-11-21 19:28:33 summary: history panel: moved refresh into 'History' header bar. Moved 'Collapse Expanded Datasets', 'Show/Hide Deleted Datasets', and 'Show/Hide Hidden Datasets' into 'History' gear menu. Removed gear menu from current history. Packed scripts. affected #: 15 files diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -183,7 +183,7 @@ _render_displayButton : function(){ // don't show display if not in ready state, error'd, or not accessible if( ( !this.model.inReadyState() ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + //|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ this.displayButton = null; diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -68,7 +68,7 @@ //TODO??: error? //TODO??: not viewable/accessible are essentially the same (not viewable set from accessible) if( ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.UPLOAD ) - || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) + //|| ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.ERROR ) || ( this.model.get( 'state' ) === HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) || ( !this.model.get( 'accessible' ) ) ){ this.editButton = null; diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/mvc/dataset/hda-model.js --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -125,6 +125,8 @@ */ inReadyState : function(){ var state = this.get( 'state' ); + //TODO: to list inclusion test + //TODO: class level readyStates list return ( ( state === HistoryDatasetAssociation.STATES.NEW ) || ( state === HistoryDatasetAssociation.STATES.OK ) diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -127,7 +127,6 @@ /** event map */ events : { - 'click #history-refresh' : function(){ window.location.reload(); }, 'click #history-tag' : 'loadAndDisplayTags' }, @@ -253,7 +252,6 @@ //NOTE: this is done before the items, since item views should handle theirs themselves newRender.append( HistoryPanel.templates.historyPanel( modelJson ) ); newRender.find( '.tooltip' ).tooltip({ placement: 'bottom' }); - this._setUpActionButton( newRender.find( '#history-action-popup' ) ); // render hda views (if any and any shown (show_deleted/hidden) //TODO: this seems too elaborate @@ -305,22 +303,6 @@ return historyView.urls; }, - /** Set up history actions popup menu - * @param {jQuery} $button jQuery dom object to turn into the 'button' that activates the menu - * @see make_popupmenu (galaxy-base.js) - */ - _setUpActionButton : function( $button ){ - var historyPanel = this, - show_deletedText = ( this.storage.get( 'show_deleted' ) )?( 'Hide deleted' ):( 'Show deleted' ), - show_hiddenText = ( this.storage.get( 'show_hidden' ) )?( 'Hide hidden' ):( 'Show hidden' ), - menuActions = {}; - //menuActions[ _l( 'refresh' ) ] = function(){ window.location.reload(); }; - menuActions[ _l( 'collapse all' ) ] = function(){ historyPanel.hideAllHdaBodies(); }; - menuActions[ _l( show_deletedText ) ] = function(){ historyPanel.toggleShowDeleted(); }; - menuActions[ _l( show_hiddenText ) ] = function(){ historyPanel.toggleShowHidden(); }; - make_popupmenu( $button, menuActions ); - }, - /** 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} $whereTo what dom element to prepend the HDA views to @@ -441,7 +423,7 @@ /** Collapse all hda bodies and clear expandedHdas in the storage */ - hideAllHdaBodies : function(){ + collapseAllHdaBodies : function(){ _.each( this.hdaViews, function( item ){ item.toggleBodyVisibility( null, false ); }); diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this._renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this,d=this.$el.find(".historyItemBody");a=(a===undefined)?(!d.is(":visible")):(a);if(a){d.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{d.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file +var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this._renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<div/>").attr("id","historyItem-"+e),d=(this.$el.children().size()===0);this.$el.attr("id","historyItemContainer-"+e);a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(this._render_body());a.append(this.body);make_popup_menus(a);a.find(".tooltip").tooltip({placement:"bottom"});this.$el.fadeOut("fast",function(){b.$el.children().remove();b.$el.append(a).fadeIn("fast",function(){b.log(b+" rendered:",b.$el);var f="rendered";if(d){f+=":initial"}else{if(b.model.inReadyState()){f+=":ready"}}b.trigger(f)})});return this},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(this.model.toJSON())))},_render_titleBar:function(){var a=$('<div class="historyItemTitleBar" style="overflow: hidden"></div>');a.append(this._render_titleButtons());a.append('<span class="state-icon"></span>');a.append(this._render_titleLink());return a},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$el},_render_titleLink:function(){return $(jQuery.trim(HDABaseView.templates.titleLink(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});return HDABaseView.templates.hdaSummary(a)},_render_primaryActionButtons:function(c){var a=this,b=$("<div/>").attr("id","primary-actions-"+this.model.get("id"));_.each(c,function(d){b.append(d.call(a))});return b},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var a=HDABaseView.templates.downloadLinks(_.extend(this.model.toJSON(),{urls:this.urls}));return $(a)},_render_showParamsButton:function(){this.showParamsButton=new IconButtonView({model:new IconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",icon_class:"information"})});return this.showParamsButton.render().$el},_render_displayApps:function(){if(!this.model.hasData()){return null}var a=$("<div/>").addClass("display-apps");if(!_.isEmpty(this.model.get("display_types"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_types")}))}if(!_.isEmpty(this.model.get("display_apps"))){a.append(HDABaseView.templates.displayApps({displayApps:this.model.get("display_apps")}))}return a},_render_peek:function(){if(!this.model.get("peek")){return null}return $("<div/>").append($("<pre/>").attr("id","peek"+this.model.get("id")).addClass("peek").append(this.model.get("peek")))},_render_body:function(){var a=$("<div/>").attr("id","info-"+this.model.get("id")).addClass("historyItemBody").attr("style","display: block");switch(this.model.get("state")){case HistoryDatasetAssociation.STATES.NOT_VIEWABLE:this._render_body_not_viewable(a);break;case HistoryDatasetAssociation.STATES.UPLOAD:this._render_body_uploading(a);break;case HistoryDatasetAssociation.STATES.PAUSED:this._render_body_paused(a);break;case HistoryDatasetAssociation.STATES.QUEUED:this._render_body_queued(a);break;case HistoryDatasetAssociation.STATES.RUNNING:this._render_body_running(a);break;case HistoryDatasetAssociation.STATES.ERROR:this._render_body_error(a);break;case HistoryDatasetAssociation.STATES.DISCARDED:this._render_body_discarded(a);break;case HistoryDatasetAssociation.STATES.SETTING_METADATA:this._render_body_setting_metadata(a);break;case HistoryDatasetAssociation.STATES.EMPTY:this._render_body_empty(a);break;case HistoryDatasetAssociation.STATES.FAILED_METADATA:this._render_body_failed_metadata(a);break;case HistoryDatasetAssociation.STATES.OK:this._render_body_ok(a);break;default:a.append($('<div>Error: unknown dataset state "'+state+'".</div>'))}a.append('<div style="clear: both"></div>');if(this.expanded){a.show()}else{a.hide()}return a},_render_body_not_viewable:function(a){a.append($("<div>"+_l("You do not have permission to view dataset")+".</div>"))},_render_body_uploading:function(a){a.append($("<div>"+_l("Dataset is uploading")+"</div>"))},_render_body_queued:function(a){a.append($("<div>"+_l("Job is waiting to run")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_paused:function(a){a.append($("<div>"+_l("Job is paused. Use the history menu to unpause")+".</div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_running:function(a){a.append("<div>"+_l("Job is currently running")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_error:function(a){if(!this.model.get("purged")){a.append($("<div>"+this.model.get("misc_blurb")+"</div>"))}a.append((_l("An error occurred running this job")+": <i>"+$.trim(this.model.get("misc_info"))+"</i>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton])))},_render_body_discarded:function(a){a.append("<div>"+_l("The job creating this dataset was cancelled before completion")+".</div>");a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_setting_metadata:function(a){a.append($("<div>"+_l("Metadata is being auto-detected")+".</div>"))},_render_body_empty:function(a){a.append($("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>"));a.append(this._render_primaryActionButtons(this.defaultPrimaryActionButtonRenderers))},_render_body_failed_metadata:function(a){a.append($(HDABaseView.templates.failedMetadata(this.model.toJSON())));this._render_body_ok(a)},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton]));a.append('<div class="clear"/>');a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility"},toggleBodyVisibility:function(c,a){var b=this,d=this.$el.find(".historyItemBody");a=(a===undefined)?(!d.is(":visible")):(a);if(a){d.slideDown("fast",function(){b.trigger("body-expanded",b.model.get("id"))})}else{d.slideUp("fast",function(){b.trigger("body-collapsed",b.model.get("id"))})}},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+a+")"}});HDABaseView.templates={warningMsg:Handlebars.templates["template-warningmessagesmall"],messages:Handlebars.templates["template-hda-warning-messages"],titleLink:Handlebars.templates["template-hda-titleLink"],hdaSummary:Handlebars.templates["template-hda-hdaSummary"],downloadLinks:Handlebars.templates["template-hda-downloadLinks"],failedMetadata:Handlebars.templates["template-hda-failedMetadata"],displayApps:Handlebars.templates["template-hda-displayApps"]}; \ No newline at end of file diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.ERROR)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a={title:_l("Delete"),href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a={title:_l("Delete"),href:this.urls["delete"],id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete"};if(this.model.get("deleted")||this.model.get("purged")){a={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(a)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var c=this.model.get("dbkey"),a=this.model.get("visualizations"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(!(this.model.hasData())||!(a&&a.length)||!(f)){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:f,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");if(c){g.dbkey=c}function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){window.parent.location=f+"/"+h+"?"+$.param(g)}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})))},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayApps());a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(b){this.log(this+".loadAndDisplayTags",b);var c=this.$el.find(".tag-area"),a=c.find(".tag-elt");if(c.is(":hidden")){if(!jQuery.trim(a.html())){$.ajax({url:this.urls.tags.get,error:function(){alert(_l("Tagging failed"))},success:function(d){a.html(d);a.find(".tooltip").tooltip();c.slideDown("fast")}})}else{c.slideDown("fast")}}else{c.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){alert(_l("Annotations failed"))},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find(".tooltip").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){var d=$(window.parent.document).find("iframe#galaxy_main"),c=a+"/scatterplot?"+$.param(b);d.attr("src",c);$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d.dbkey=b}$.ajax({url:a+"/list_tracks?f-"+$.param(d),dataType:"html",error:function(){alert(_l("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.show_modal(_l("View Data in a New or Saved Visualization"),"",{Cancel:function(){f.hide_modal()},"View in saved visualization":function(){f.show_modal(_l("Add Data to Saved Visualization"),e,{Cancel:function(){f.hide_modal()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){var g=$(this).val();c.id=g;f.location=a+"/trackster?"+$.param(c)})}})},"View in new visualization":function(){f.location=a+"/trackster?"+$.param(c)}})}});return false}}; \ No newline at end of file diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 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 @@ -var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-refresh":function(){window.location.reload()},"click #history-tag":"loadAndDisplayTags"},initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("(init'd) this.storage:",this.storage.get())},add:function(a){},addAll:function(){this.render()},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});this._setUpActionButton(c.find("#history-action-popup"));if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},_setUpActionButton:function(e){var c=this,d=(this.storage.get("show_deleted"))?("Hide deleted"):("Show deleted"),a=(this.storage.get("show_hidden"))?("Hide hidden"):("Show hidden"),b={};b[_l("collapse all")]=function(){c.hideAllHdaBodies()};b[_l(d)]=function(){c.toggleShowDeleted()};b[_l(a)]=function(){c.toggleShowHidden()};make_popupmenu(e,b)},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},hideAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=BaseView.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags"},initialize:function(a){this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.hdaViews={};this.urls={}},_setUpWebStorage:function(b,a,c){this.storage=new PersistantStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log("this.storage:",this.storage.get());if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log("(init'd) this.storage:",this.storage.get())},add:function(a){},addAll:function(){this.render()},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find(".tooltip").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render()},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render()},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var d=this.$el.find("#history-tag-area"),b=d.find(".tag-elt");this.log("\t tagArea",d," tagElt",b);if(d.is(":hidden")){if(!jQuery.trim(b.html())){var a=this;$.ajax({url:a.urls.tag,error:function(){alert(_l("Tagging failed"))},success:function(e){b.html(e);b.find(".tooltip").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/packed/templates/compiled/template-history-historyPanel.js --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(j,C,A,r,J){A=A||j.helpers;var B="",n,m,x=this,f="function",c=A.blockHelperMissing,e=this.escapeExpression;function u(O,N){var L="",M,K;L+='\n <div id="history-name" class="tooltip editable-text"\n title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(2,t,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(2,t,N)})}if(M||M===0){L+=M}L+='">';K=A.name;if(K){M=K.call(O,{hash:{}})}else{M=O.name;M=typeof M===f?M():M}L+=e(M)+"</div>\n ";return L}function t(L,K){return"Click to rename history"}function s(O,N){var L="",M,K;L+='\n <div id="history-name" class="tooltip"\n title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(5,q,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(5,q,N)})}if(M||M===0){L+=M}L+='">';K=A.name;if(K){M=K.call(O,{hash:{}})}else{M=O.name;M=typeof M===f?M():M}L+=e(M)+"</div>\n ";return L}function q(L,K){return"You must be logged in to edit your history name"}function p(O,N){var L="",M,K;L+='\n <a id="history-tag" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(8,l,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(8,l,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(10,I,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(10,I,N)})}if(M||M===0){L+=M}L+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n ';return L}function l(L,K){return"Edit history tags"}function I(L,K){return"Edit history annotation"}function H(L,K){return"Refresh this display"}function G(L,K){return"Click to see more actions for this history"}function F(O,N){var L="",M,K;L+="\n ";K=A.warningmessagesmall;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(17,E,N)})}else{M=O.warningmessagesmall;M=typeof M===f?M():M}if(!A.warningmessagesmall){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(17,E,N)})}if(M||M===0){L+=M}L+="\n ";return L}function E(N,M){var L,K;K=A.local;if(K){L=K.call(N,{hash:{},inverse:x.noop,fn:x.program(18,D,M)})}else{L=N.local;L=typeof L===f?L():L}if(!A.local){L=c.call(N,L,{hash:{},inverse:x.noop,fn:x.program(18,D,M)})}if(L||L===0){return L}else{return""}}function D(L,K){return"You are currently viewing a deleted history!"}function o(O,N){var L="",M,K;L+='\n <div id="history-tag-annotation">\n\n <div id="history-tag-area" style="display: none">\n <strong>';K=A.local;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(21,k,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(21,k,N)})}if(M||M===0){L+=M}L+=':</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>';K=A.local;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(23,i,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(23,i,N)})}if(M||M===0){L+=M}L+=':</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text"\n title="';K=A.local;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(25,h,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(25,h,N)})}if(M||M===0){L+=M}L+='">\n ';M=O.annotation;M=A["if"].call(O,M,{hash:{},inverse:x.program(29,d,N),fn:x.program(27,g,N)});if(M||M===0){L+=M}L+="\n </div>\n </div>\n </div>\n </div>\n ";return L}function k(L,K){return"Tags"}function i(L,K){return"Annotation"}function h(L,K){return"Click to edit annotation"}function g(O,N){var L="",M,K;L+="\n ";K=A.annotation;if(K){M=K.call(O,{hash:{}})}else{M=O.annotation;M=typeof M===f?M():M}L+=e(M)+"\n ";return L}function d(O,N){var L="",M,K;L+="\n <em>";K=A.local;if(K){M=K.call(O,{hash:{},inverse:x.noop,fn:x.program(30,z,N)})}else{M=O.local;M=typeof M===f?M():M}if(!A.local){M=c.call(O,M,{hash:{},inverse:x.noop,fn:x.program(30,z,N)})}if(M||M===0){L+=M}L+="</em>\n ";return L}function z(L,K){return"Describe or add notes to history"}function y(O,N){var L="",M,K;L+='\n <div id="message-container">\n <div class="';K=A.status;if(K){M=K.call(O,{hash:{}})}else{M=O.status;M=typeof M===f?M():M}L+=e(M)+'message">\n ';K=A.message;if(K){M=K.call(O,{hash:{}})}else{M=O.message;M=typeof M===f?M():M}L+=e(M)+"\n </div><br />\n </div>\n ";return L}function w(L,K){return"You are over your disk quota.\n Tool execution is on hold until your disk usage drops below your allocated quota."}function v(L,K){return"Your history is empty. Click 'Get Data' on the left pane to start"}B+='<div id="history-controls">\n <div id="history-title-area" class="historyLinks">\n\n ';B+='\n <div id="history-name-container">\n ';B+="\n ";n=C.user;n=n==null||n===false?n:n.email;n=A["if"].call(C,n,{hash:{},inverse:x.program(4,s,J),fn:x.program(1,u,J)});if(n||n===0){B+=n}B+='\n </div>\n </div>\n\n <div id="history-subtitle-area">\n <div id="history-size" style="float:left;">';m=A.nice_size;if(m){n=m.call(C,{hash:{}})}else{n=C.nice_size;n=typeof n===f?n():n}B+=e(n)+'</div>\n\n <div id="history-secondary-links" style="float: right;">\n ';n=C.user;n=n==null||n===false?n:n.email;n=A["if"].call(C,n,{hash:{},inverse:x.noop,fn:x.program(7,p,J)});if(n||n===0){B+=n}B+='\n <a id="history-refresh" class="tooltip" title="';m=A.local;if(m){n=m.call(C,{hash:{},inverse:x.noop,fn:x.program(12,H,J)})}else{n=C.local;n=typeof n===f?n():n}if(!A.local){n=c.call(C,n,{hash:{},inverse:x.noop,fn:x.program(12,H,J)})}if(n||n===0){B+=n}B+='"\n href="javascript:void(0);">\n <span class="ficon refresh large"></span>\n </a>\n <a id="history-action-popup" class="tooltip" title="';m=A.local;if(m){n=m.call(C,{hash:{},inverse:x.noop,fn:x.program(14,G,J)})}else{n=C.local;n=typeof n===f?n():n}if(!A.local){n=c.call(C,n,{hash:{},inverse:x.noop,fn:x.program(14,G,J)})}if(n||n===0){B+=n}B+='"\n href="javascript:void(0);">\n <span class="ficon cogs large"></span>\n </a>\n </div>\n <div style="clear: both;"></div>\n </div>\n\n ';n=C.deleted;n=A["if"].call(C,n,{hash:{},inverse:x.noop,fn:x.program(16,F,J)});if(n||n===0){B+=n}B+="\n\n ";B+="\n ";B+="\n ";n=C.user;n=n==null||n===false?n:n.email;n=A["if"].call(C,n,{hash:{},inverse:x.noop,fn:x.program(20,o,J)});if(n||n===0){B+=n}B+="\n\n ";n=C.message;n=A["if"].call(C,n,{hash:{},inverse:x.noop,fn:x.program(32,y,J)});if(n||n===0){B+=n}B+='\n\n <div id="quota-message-container" style="display: none">\n <div id="quota-message" class="errormessage">\n ';m=A.local;if(m){n=m.call(C,{hash:{},inverse:x.noop,fn:x.program(34,w,J)})}else{n=C.local;n=typeof n===f?n():n}if(!A.local){n=c.call(C,n,{hash:{},inverse:x.noop,fn:x.program(34,w,J)})}if(n||n===0){B+=n}B+='\n </div>\n </div>\n</div>\n\n<div id="';m=A.id;if(m){n=m.call(C,{hash:{}})}else{n=C.id;n=typeof n===f?n():n}B+=e(n)+'-datasets" class="history-datasets-list"></div>\n\n<div class="infomessagesmall" id="emptyHistoryMessage" style="display: none;">\n ';m=A.local;if(m){n=m.call(C,{hash:{},inverse:x.noop,fn:x.program(36,v,J)})}else{n=C.local;n=typeof n===f?n():n}if(!A.local){n=c.call(C,n,{hash:{},inverse:x.noop,fn:x.program(36,v,J)})}if(n||n===0){B+=n}B+="\n</div>";return B})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(j,z,x,q,H){x=x||j.helpers;var y="",n,m,u=this,e="function",c=x.blockHelperMissing,d=this.escapeExpression;function t(M,L){var J="",K,I;J+='\n <div id="history-name" class="tooltip editable-text"\n title="';I=x.local;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(2,s,L)})}else{K=M.local;K=typeof K===e?K():K}if(!x.local){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(2,s,L)})}if(K||K===0){J+=K}J+='">';I=x.name;if(I){K=I.call(M,{hash:{}})}else{K=M.name;K=typeof K===e?K():K}J+=d(K)+"</div>\n ";return J}function s(J,I){return"Click to rename history"}function r(M,L){var J="",K,I;J+='\n <div id="history-name" class="tooltip"\n title="';I=x.local;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(5,p,L)})}else{K=M.local;K=typeof K===e?K():K}if(!x.local){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(5,p,L)})}if(K||K===0){J+=K}J+='">';I=x.name;if(I){K=I.call(M,{hash:{}})}else{K=M.name;K=typeof K===e?K():K}J+=d(K)+"</div>\n ";return J}function p(J,I){return"You must be logged in to edit your history name"}function o(M,L){var J="",K,I;J+='\n <a id="history-tag" title="';I=x.local;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(8,l,L)})}else{K=M.local;K=typeof K===e?K():K}if(!x.local){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(8,l,L)})}if(K||K===0){J+=K}J+='"\n class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n <a id="history-annotate" title="';I=x.local;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(10,G,L)})}else{K=M.local;K=typeof K===e?K():K}if(!x.local){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(10,G,L)})}if(K||K===0){J+=K}J+='"\n class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a>\n ';return J}function l(J,I){return"Edit history tags"}function G(J,I){return"Edit history annotation"}function F(M,L){var J="",K,I;J+="\n ";I=x.warningmessagesmall;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(13,E,L)})}else{K=M.warningmessagesmall;K=typeof K===e?K():K}if(!x.warningmessagesmall){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(13,E,L)})}if(K||K===0){J+=K}J+="\n ";return J}function E(L,K){var J,I;I=x.local;if(I){J=I.call(L,{hash:{},inverse:u.noop,fn:u.program(14,D,K)})}else{J=L.local;J=typeof J===e?J():J}if(!x.local){J=c.call(L,J,{hash:{},inverse:u.noop,fn:u.program(14,D,K)})}if(J||J===0){return J}else{return""}}function D(J,I){return"You are currently viewing a deleted history!"}function C(M,L){var J="",K,I;J+='\n <div id="history-tag-annotation">\n\n <div id="history-tag-area" style="display: none">\n <strong>';I=x.local;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(17,B,L)})}else{K=M.local;K=typeof K===e?K():K}if(!x.local){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(17,B,L)})}if(K||K===0){J+=K}J+=':</strong>\n <div class="tag-elt"></div>\n </div>\n\n <div id="history-annotation-area" style="display: none">\n <strong>';I=x.local;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(19,A,L)})}else{K=M.local;K=typeof K===e?K():K}if(!x.local){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(19,A,L)})}if(K||K===0){J+=K}J+=':</strong>\n <div id="history-annotation-container">\n <div id="history-annotation" class="tooltip editable-text"\n title="';I=x.local;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(21,k,L)})}else{K=M.local;K=typeof K===e?K():K}if(!x.local){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(21,k,L)})}if(K||K===0){J+=K}J+='">\n ';K=M.annotation;K=x["if"].call(M,K,{hash:{},inverse:u.program(25,h,L),fn:u.program(23,i,L)});if(K||K===0){J+=K}J+="\n </div>\n </div>\n </div>\n </div>\n ";return J}function B(J,I){return"Tags"}function A(J,I){return"Annotation"}function k(J,I){return"Click to edit annotation"}function i(M,L){var J="",K,I;J+="\n ";I=x.annotation;if(I){K=I.call(M,{hash:{}})}else{K=M.annotation;K=typeof K===e?K():K}J+=d(K)+"\n ";return J}function h(M,L){var J="",K,I;J+="\n <em>";I=x.local;if(I){K=I.call(M,{hash:{},inverse:u.noop,fn:u.program(26,g,L)})}else{K=M.local;K=typeof K===e?K():K}if(!x.local){K=c.call(M,K,{hash:{},inverse:u.noop,fn:u.program(26,g,L)})}if(K||K===0){J+=K}J+="</em>\n ";return J}function g(J,I){return"Describe or add notes to history"}function f(M,L){var J="",K,I;J+='\n <div id="message-container">\n <div class="';I=x.status;if(I){K=I.call(M,{hash:{}})}else{K=M.status;K=typeof K===e?K():K}J+=d(K)+'message">\n ';I=x.message;if(I){K=I.call(M,{hash:{}})}else{K=M.message;K=typeof K===e?K():K}J+=d(K)+"\n </div><br />\n </div>\n ";return J}function w(J,I){return"You are over your disk quota.\n Tool execution is on hold until your disk usage drops below your allocated quota."}function v(J,I){return"Your history is empty. Click 'Get Data' on the left pane to start"}y+='<div id="history-controls">\n <div id="history-title-area" class="historyLinks">\n\n ';y+='\n <div id="history-name-container">\n ';y+="\n ";n=z.user;n=n==null||n===false?n:n.email;n=x["if"].call(z,n,{hash:{},inverse:u.program(4,r,H),fn:u.program(1,t,H)});if(n||n===0){y+=n}y+='\n </div>\n </div>\n\n <div id="history-subtitle-area">\n <div id="history-size" style="float:left;">';m=x.nice_size;if(m){n=m.call(z,{hash:{}})}else{n=z.nice_size;n=typeof n===e?n():n}y+=d(n)+'</div>\n\n <div id="history-secondary-links" style="float: right;">\n ';n=z.user;n=n==null||n===false?n:n.email;n=x["if"].call(z,n,{hash:{},inverse:u.noop,fn:u.program(7,o,H)});if(n||n===0){y+=n}y+='\n </div>\n <div style="clear: both;"></div>\n </div>\n\n ';n=z.deleted;n=x["if"].call(z,n,{hash:{},inverse:u.noop,fn:u.program(12,F,H)});if(n||n===0){y+=n}y+="\n\n ";y+="\n ";y+="\n ";n=z.user;n=n==null||n===false?n:n.email;n=x["if"].call(z,n,{hash:{},inverse:u.noop,fn:u.program(16,C,H)});if(n||n===0){y+=n}y+="\n\n ";n=z.message;n=x["if"].call(z,n,{hash:{},inverse:u.noop,fn:u.program(28,f,H)});if(n||n===0){y+=n}y+='\n\n <div id="quota-message-container" style="display: none">\n <div id="quota-message" class="errormessage">\n ';m=x.local;if(m){n=m.call(z,{hash:{},inverse:u.noop,fn:u.program(30,w,H)})}else{n=z.local;n=typeof n===e?n():n}if(!x.local){n=c.call(z,n,{hash:{},inverse:u.noop,fn:u.program(30,w,H)})}if(n||n===0){y+=n}y+='\n </div>\n </div>\n</div>\n\n<div id="';m=x.id;if(m){n=m.call(z,{hash:{}})}else{n=z.id;n=typeof n===e?n():n}y+=d(n)+'-datasets" class="history-datasets-list"></div>\n\n<div class="infomessagesmall" id="emptyHistoryMessage" style="display: none;">\n ';m=x.local;if(m){n=m.call(z,{hash:{},inverse:u.noop,fn:u.program(32,v,H)})}else{n=z.local;n=typeof n===e?n():n}if(!x.local){n=c.call(z,n,{hash:{},inverse:u.noop,fn:u.program(32,v,H)})}if(n||n===0){y+=n}y+="\n</div>";return y})})(); \ No newline at end of file diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js --- a/static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js +++ b/static/scripts/packed/templates/compiled/template-visualization-scatterplotControlForm.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-scatterplotControlForm"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}function c(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}function o(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}j+='\n\n<ul class="nav nav-tabs">\n <li class="active">\n <a data-toggle="tab" href="#data-settings">Data Controls</a>\n </li>\n <li><a data-toggle="tab" href="#chart-settings">Plot Controls</a></li>\n <li><a data-toggle="tab" href="#chart-stats">Statistics</a></li>\n</ul>\n\n';j+='\n<div class="tab-content">\n<div id="data-settings" class="tab-pane active">\n\n <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 ';j+='\n <div class="column-select">\n <label for="X-select">Data column for X: </label>\n <select name="X" id="X-select">\n ';d=n.numericColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(1,e,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n <div class="column-select">\n <label for="Y-select">Data column for Y: </label>\n <select name="Y" id="Y-select">\n ';d=n.numericColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(3,c,l)});if(d||d===0){j+=d}j+="\n </select>\n </div>\n \n ";j+='\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="ID" id="ID-select">\n ';d=n.allColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(5,o,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n \n <input id="render-button" type="button" value="Draw" />\n <input id="save-button" type="button" value="Download Plot as SVG" style="display: none;" />\n <div class="clear"></div>\n</div>\n\n<div id="chart-settings" class="tab-pane">\n</div>\n\n<div id="chart-stats" class="tab-pane">\n</div>\n</div>';j+="\n\n";j+='\n<div id="loading-indicator" style="display: none;">\n <img class="loading-img" src="';i=f.loadingIndicatorImagePath;if(i){d=i.call(n,{hash:{}})}else{d=n.loadingIndicatorImagePath;d=typeof d===h?d():d}j+=k(d)+'" />\n <span class="loading-message">';i=f.message;if(i){d=i.call(n,{hash:{}})}else{d=n.message;d=typeof d===h?d():d}j+=k(d)+"</span>\n</div>";return j})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-visualization-scatterplotControlForm"]=b(function(g,n,f,m,l){f=f||g.helpers;var j="",d,i,h="function",k=this.escapeExpression,p=this;function e(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}function c(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}function o(u,t){var r="",s,q;r+='\n <option value="';q=f.index;if(q){s=q.call(u,{hash:{}})}else{s=u.index;s=typeof s===h?s():s}r+=k(s)+'">';q=f.name;if(q){s=q.call(u,{hash:{}})}else{s=u.name;s=typeof s===h?s():s}r+=k(s)+"</option>\n ";return r}j+='\n\n<ul class="nav nav-tabs">\n <li class="active"><a data-toggle="tab" href="#data-settings">Data Controls</a></li>\n <li><a data-toggle="tab" href="#chart-settings">Plot Controls</a></li>\n <li><a data-toggle="tab" href="#chart-stats">Statistics</a></li>\n <li><a data-toggle="tab" href="#chart">Chart</a></li>\n</ul>\n\n';j+='\n<div class="tab-content">\n<div id="data-settings" class="tab-pane active">\n\n <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 ';j+='\n <div class="column-select">\n <label for="X-select">Data column for X: </label>\n <select name="X" id="X-select">\n ';d=n.numericColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(1,e,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n <div class="column-select">\n <label for="Y-select">Data column for Y: </label>\n <select name="Y" id="Y-select">\n ';d=n.numericColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(3,c,l)});if(d||d===0){j+=d}j+="\n </select>\n </div>\n \n ";j+='\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="ID" id="ID-select">\n ';d=n.allColumns;d=f.each.call(n,d,{hash:{},inverse:p.noop,fn:p.program(5,o,l)});if(d||d===0){j+=d}j+='\n </select>\n </div>\n \n <input id="render-button" type="button" value="Draw" />\n <input id="save-button" type="button" value="Download Plot as SVG" style="display: none;" />\n <div class="clear"></div>\n</div>\n\n<div id="chart-settings" class="tab-pane">\n</div>\n\n<div id="chart-stats" class="tab-pane">\n</div>\n</div>';j+="\n\n";j+='\n<div id="loading-indicator" style="display: none;">\n <img class="loading-img" src="';i=f.loadingIndicatorImagePath;if(i){d=i.call(n,{hash:{}})}else{d=n.loadingIndicatorImagePath;d=typeof d===h?d():d}j+=k(d)+'" />\n <span class="loading-message">';i=f.message;if(i){d=i.call(n,{hash:{}})}else{d=n.message;d=typeof d===h?d():d}j+=k(d)+"</span>\n</div>";return j})})(); \ No newline at end of file diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","../templates/compiled/template-visualization-scatterplotControlForm","../templates/compiled/template-visualization-statsTable","../templates/compiled/template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../libs/jquery/jquery-ui"],function(){function a(f){var d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(console,i)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(i,j){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart");this.content=this.svg.append("svg:g").attr("class","content").attr("id",this.config.id);this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.adjustChartDimensions=function(l,j,i,k){l=l||0;j=j||0;i=i||0;k=k||0;this.svg.attr("width",this.config.width+(this.config.marginRight+j)+(this.config.marginLeft+k)).attr("height",this.config.height+(this.config.marginTop+l)+(this.config.marginBottom+i)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+k,this.config.marginTop+l))};this.preprocessData=function(k,j,i){return(k.length>this.config.maxDataPoints)?(k.slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains=function(i,k,j){this.xMin=this.config.xMin||(j)?(j[0].min):(d3.min(i));this.xMax=this.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=this.config.yMin||(j)?(j[1].min):(d3.min(k));this.yMax=this.config.yMax||(j)?(j[1].max):(d3.max(k))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);var i=this.yAxis.selectAll("text").filter(function(m,l){return l!==0});this.yLongestLabel=d3.max(i[0].map(function(m,l){return(d3.select(m).text()).length}))||0;var j=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(j-g);if(this.config.marginLeft<j){var k=(j)-this.config.marginLeft;k=(k<0)?(0):(k);this.adjustChartDimensions(0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(i){};this.glyphFinalState=function(i){};this.glyphExitState=function(i){};this.renderDatapoints=function(i,l,j){this.log(this+".renderDatapoints",arguments);var k=0;this.datapoints=this.addDatapoints(i,l,j,".glyph");this.datapoints.exit().each(function(){k+=1}).transition().duration(this.config.animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs removed")};this.addDatapoints=function(m,k,i,l){this.log(this+".addDatapoints",arguments);var p=this,o=0,q=function(s,r){return p.xScale(m[r])},j=function(s,r){return p.yScale(k[r])};var n=this.content.selectAll(l);this.log("existing datapoints:",n);n=n.data(m);o=0;n.enter().append("svg:circle").each(function(){o+=1}).classed("glyph",true).attr("cx",q).attr("cy",j).attr("r",0);this.log(o," new glyphs created");o=0;n.transition().duration(this.config.animDuration).each(function(){o+=1}).attr("cx",q).attr("cy",j).attr("r",p.config.datapointSize);this.log(o," existing glyphs transitioned");if(i){n.attr("data",function(s,r){return(i[r])})}n.attr("title",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]});n.on("mouseover",function(t,r){var s=d3.select(this);s.style("fill","red").style("fill-opacity",1);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",s.attr("cx")).attr("y1",s.attr("cy")).attr("x2",0).attr("y2",s.attr("cy")).classed("hoverline",true);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",s.attr("cx")).attr("y1",s.attr("cy")).attr("x2",s.attr("cx")).attr("y2",p.config.height).classed("hoverline",true)}).on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return n};this.render=function(k,l){this.log(this+".render",arguments);var i=k[0],m=k[1],j=(k.length>2)?(k[2]):(undefined);i=this.preprocessData(i);m=this.preprocessData(m);this.log("xCol len",i.length,"yCol len",m.length);this.setUpDomains(i,m,l);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,m,j)}}var b=BaseView.extend(LoggableMixin).extend({className:"scatterplot-settings-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"loading_large_white_bg.gif",initialize:function(c){this.log(this+".initialize, attributes:",c);this.dataset=null;this.chartConfig=null;this.plot=null;this.loader=null;this.$statsPanel=null;this.$chartSettingsPanel=null;this.$dataSettingsPanel=null;this.dataFetch=null;this.initializeFromAttributes(c);this.initializeChart(c);this.initializeDataLoader(c)},initializeFromAttributes:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("dataset:",this.dataset);if(!c.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=c.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("this.dataURL:",this.dataURL)},initializeChart:function(c){this.chartConfig=c.chartConfig||{};if(this.logger){this.chartConfig.debugging=true}this.log("initial chartConfig:",this.chartConfig);this.plot=new a(this.chartConfig);this.chartConfig=this.plot.config},initializeDataLoader:function(d){var c=this;this.loader=new LazyDataLoader({logger:(this.logger)?(this.logger):(null),url:null,start:d.start||0,total:d.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})}});$(this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);alert("ERROR fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:function(){var c=this,d={config:this.chartConfig,allColumns:[],numericColumns:[],loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage};_.each(this.dataset.metadata_column_types,function(g,f){var e="column "+(f+1);if(c.dataset.metadata_column_names){e=c.dataset.metadata_column_names[f]}if(g==="int"||g==="float"){d.numericColumns.push({index:(f+1),name:e})}d.allColumns.push({index:(f+1),name:e})});this.$el.append(b.templates.form(d));this.$dataSettingsPanel=this.$el.find(".tab-pane#data-settings");this.$chartSettingsPanel=this._render_chartSettings();this.$statsPanel=this.$el.find(".tab-pane#chart-stats");this.$dataSettingsPanel.find("#X-select").val(this.chartConfig.xColumn);this.$dataSettingsPanel.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked",true).trigger("change");this.$dataSettingsPanel.find("#ID-select").val(this.chartConfig.idColumn)}if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderPlot()}return this},isColumnNumeric:function(c){if((c>=0)&&(c<this.dataset.metadata_column_types.length)){var d=this.dataset.metadata_column_types[c];return(d==="int"||d==="float")}return false},_render_chartSettings:function(){var c=this,d=this.$el.find(".tab-pane#chart-settings"),e={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};d.append(b.templates.chartSettings(this.chartConfig));d.find(".numeric-slider-input").each(function(){var h=$(this),g=h.find(".slider-output"),i=h.find(".slider"),j=h.attr("id");function f(){var l=$(this),k=l.slider("value");g.text(k)}i.slider(_.extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-settings #render-button":"renderPlot","click #chart-settings #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},showLoadingIndicator:function(d,e){d=d||"";var c=this.$el.find("div#loading-indicator");messageBox=c.find(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut("fast",function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e()}}else{if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:function(c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},renderPlot:function(){var c=this;c.data=null;c.meta=null;_.extend(this.chartConfig,this.getGraphSettings());this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("this.loader, url:",this.loader.url,"total:",this.loader.total);$(this.loader).bind("loaded.new",function(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse(d);c.log("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicator("Rendering...",function(){c.$el.find("ul.nav").find('a[href="#chart-stats"]').tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.meta);c.hideLoadingIndicator()})});$(this.loader).bind("complete",function(d,e){c.log("complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetching data...",function(){c.loader.load()})},renderStats:function(){this.$statsPanel.html(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var c=this;newGraphSettings=this.getGraphSettings();this.log("newGraphSettings:",newGraphSettings);_.extend(this.chartConfig,newGraphSettings);this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);if(c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.plot.render(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot()}},postProcessDataFetchResponse:function(c){this.postProcessData(c.data);this.postProcessMeta(c.meta)},postProcessData:function(d){var c=this;if(c.data){_.each(d,function(f,e){c.data[e]=c.data[e].concat(f)})}else{c.data=d}},postProcessMeta:function(e){var c=this,d=this.dataset.metadata_column_types;if(c.meta){_.each(e,function(g,f){var k=c.meta[f],i=d[f];c.log(f+" postprocessing meta:",g);k.count+=(g.count)?(g.count):(0);c.log(f,"count:",k.count);if((i==="int")||(i==="float")){k.min=Math.min(g.min,k.min);k.max=Math.max(g.max,k.max);k.sum=g.sum+k.sum;k.mean=(k.count)?(k.sum/k.count):(null);var h=c.data[f].slice().sort(),j=Math.floor(h.length/2);if(h.length%2===0){k.median=((h[j]+h[(j+1)])/2)}else{k.median=h[j]}}})}else{c.meta=e;c.log("initial meta:",c.meta)}},getDataSettings:function(){var d=this.getColumnSelections(),c=[];this.log("columnSelections:",d);c=[d.X.colIndex,d.Y.colIndex];if(this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked")){c.push(d.ID.colIndex)}var e={data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);return e},getColumnSelections:function(){var c={};this.$dataSettingsPanel.find("div.column-select select").each(function(){var d=$(this),e=d.val();c[d.attr("name")]={colIndex:e,colName:d.children('[value="'+e+'"]').text()}});return c},getGraphSettings:function(){var e={},f=this.getColumnSelections();e.datapointSize=this.$chartSettingsPanel.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");e.width=this.$chartSettingsPanel.find("#width.numeric-slider-input").find(".slider").slider("value");e.height=this.$chartSettingsPanel.find("#height.numeric-slider-input").find(".slider").slider("value");var d=this.$chartSettingsPanel.find("input#X-axis-label").val(),c=this.$chartSettingsPanel.find("input#Y-axis-label").val();e.xLabel=(d==="X")?(f.X.colName):(d);e.yLabel=(c==="Y")?(f.Y.colName):(c);e.animDuration=10;if(this.$chartSettingsPanel.find("#animDuration.checkbox-input").is(":checked")){e.animDuration=500}this.log("graphSettings:",e);return e},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});b.templates={form:Handlebars.templates["template-visualization-scatterplotControlForm"],statsTable:Handlebars.templates["template-visualization-statsTable"],chartSettings:Handlebars.templates["template-visualization-chartSettings"]};return{LazyDataLoader:LazyDataLoader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file +define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","../templates/compiled/template-visualization-scatterplotControlForm","../templates/compiled/template-visualization-statsTable","../templates/compiled/template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../libs/jquery/jquery-ui"],function(){function a(f){var d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(console,i)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(i,j){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart");this.content=this.svg.append("svg:g").attr("class","content").attr("id",this.config.id);this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.adjustChartDimensions=function(l,j,i,k){l=l||0;j=j||0;i=i||0;k=k||0;this.svg.attr("width",this.config.width+(this.config.marginRight+j)+(this.config.marginLeft+k)).attr("height",this.config.height+(this.config.marginTop+l)+(this.config.marginBottom+i)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+k,this.config.marginTop+l))};this.preprocessData=function(k,j,i){return(k.length>this.config.maxDataPoints)?(k.slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains=function(i,k,j){this.xMin=this.config.xMin||(j)?(j[0].min):(d3.min(i));this.xMax=this.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=this.config.yMin||(j)?(j[1].min):(d3.min(k));this.yMax=this.config.yMax||(j)?(j[1].max):(d3.max(k))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);var i=this.yAxis.selectAll("text").filter(function(m,l){return l!==0});this.yLongestLabel=d3.max(i[0].map(function(m,l){return(d3.select(m).text()).length}))||0;var j=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(j-g);if(this.config.marginLeft<j){var k=(j)-this.config.marginLeft;k=(k<0)?(0):(k);this.adjustChartDimensions(0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(i){};this.glyphFinalState=function(i){};this.glyphExitState=function(i){};this.renderDatapoints=function(i,l,j){this.log(this+".renderDatapoints",arguments);var k=0;this.datapoints=this.addDatapoints(i,l,j,".glyph");this.datapoints.exit().each(function(){k+=1}).transition().duration(this.config.animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs removed")};this.addDatapoints=function(m,k,i,l){this.log(this+".addDatapoints",arguments);var p=this,o=0,q=function(s,r){return p.xScale(m[r])},j=function(s,r){return p.yScale(k[r])};var n=this.content.selectAll(l);this.log("existing datapoints:",n);n=n.data(m);o=0;n.enter().append("svg:circle").each(function(){o+=1}).classed("glyph",true).attr("cx",q).attr("cy",j).attr("r",0);this.log(o," new glyphs created");o=0;n.transition().duration(this.config.animDuration).each(function(){o+=1}).attr("cx",q).attr("cy",j).attr("r",p.config.datapointSize);this.log(o," existing glyphs transitioned");if(i){n.attr("data",function(s,r){return(i[r])})}n.attr("title",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]});n.on("mouseover",function(t,r){var s=d3.select(this);s.style("fill","red").style("fill-opacity",1);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",s.attr("cx")).attr("y1",s.attr("cy")).attr("x2",0).attr("y2",s.attr("cy")).classed("hoverline",true);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",s.attr("cx")).attr("y1",s.attr("cy")).attr("x2",s.attr("cx")).attr("y2",p.config.height).classed("hoverline",true)}).on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return n};this.render=function(k,l){this.log(this+".render",arguments);var i=k[0],m=k[1],j=(k.length>2)?(k[2]):(undefined);i=this.preprocessData(i);m=this.preprocessData(m);this.log("xCol len",i.length,"yCol len",m.length);this.setUpDomains(i,m,l);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,m,j)}}var b=BaseView.extend(LoggableMixin).extend({className:"scatterplot-settings-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"loading_large_white_bg.gif",initialize:function(c){this.log(this+".initialize, attributes:",c);this.dataset=null;this.chartConfig=null;this.plot=null;this.loader=null;this.$statsPanel=null;this.$chartSettingsPanel=null;this.$dataSettingsPanel=null;this.dataFetch=null;this.initializeFromAttributes(c);this.initializeChart(c);this.initializeDataLoader(c)},initializeFromAttributes:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("dataset:",this.dataset);if(!c.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=c.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("this.dataURL:",this.dataURL)},initializeChart:function(c){this.chartConfig=c.chartConfig||{};if(this.logger){this.chartConfig.debugging=true}this.log("initial chartConfig:",this.chartConfig);this.plot=new a(this.chartConfig);this.chartConfig=this.plot.config},initializeDataLoader:function(d){var c=this;this.loader=new LazyDataLoader({logger:(this.logger)?(this.logger):(null),url:null,start:d.start||0,total:d.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})}});$(this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);alert("ERROR fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:function(){var c=this,d={config:this.chartConfig,allColumns:[],numericColumns:[],loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage};_.each(this.dataset.metadata_column_types,function(g,f){var e="column "+(f+1);if(c.dataset.metadata_column_names){e=c.dataset.metadata_column_names[f]}if(g==="int"||g==="float"){d.numericColumns.push({index:(f+1),name:e})}d.allColumns.push({index:(f+1),name:e})});this.$el.append(b.templates.form(d));this.$dataSettingsPanel=this.$el.find(".tab-pane#data-settings");this.$chartSettingsPanel=this._render_chartSettings();this.$statsPanel=this.$el.find(".tab-pane#chart-stats");this.$dataSettingsPanel.find("#X-select").val(this.chartConfig.xColumn);this.$dataSettingsPanel.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked",true).trigger("change");this.$dataSettingsPanel.find("#ID-select").val(this.chartConfig.idColumn)}if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderPlot()}return this},isColumnNumeric:function(c){if((c>=0)&&(c<this.dataset.metadata_column_types.length)){var d=this.dataset.metadata_column_types[c];return(d==="int"||d==="float")}return false},_render_chartSettings:function(){var c=this,d=this.$el.find(".tab-pane#chart-settings"),e={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};d.append(b.templates.chartSettings(this.chartConfig));d.find(".numeric-slider-input").each(function(){var h=$(this),g=h.find(".slider-output"),i=h.find(".slider"),j=h.attr("id");function f(){var l=$(this),k=l.slider("value");g.text(k)}i.slider(_.extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-settings #render-button":"renderPlot","click #chart-settings #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},showLoadingIndicator:function(d,e){d=d||"";var c=this.$el.find("div#loading-indicator");messageBox=c.find(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut("fast",function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e()}}else{if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:function(c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},renderPlot:function(){var c=this;c.data=null;c.meta=null;_.extend(this.chartConfig,this.getGraphSettings());this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("this.loader, url:",this.loader.url,"total:",this.loader.total);$(this.loader).bind("loaded.new",function(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse(d);c.log("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicator("Rendering...",function(){c.$el.find("ul.nav").find('a[href="#chart-stats"]').tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.meta);c.hideLoadingIndicator()})});$(this.loader).bind("complete",function(d,e){c.log("complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetching data...",function(){c.loader.load()})},renderStats:function(){this.$statsPanel.html(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var c=this;newGraphSettings=this.getGraphSettings();this.log("newGraphSettings:",newGraphSettings);_.extend(this.chartConfig,newGraphSettings);this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);if(c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.plot.render(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot()}},postProcessDataFetchResponse:function(c){this.postProcessData(c.data);this.postProcessMeta(c.meta)},postProcessData:function(d){var c=this;if(c.data){_.each(d,function(f,e){c.data[e]=c.data[e].concat(f)})}else{c.data=d}},postProcessMeta:function(e){var c=this,d=this.dataset.metadata_column_types;if(c.meta){_.each(e,function(g,f){var k=c.meta[f],i=d[f];c.log(f+" postprocessing meta:",g);k.count+=(g.count)?(g.count):(0);c.log(f,"count:",k.count);if((i==="int")||(i==="float")){k.min=Math.min(g.min,k.min);k.max=Math.max(g.max,k.max);k.sum=g.sum+k.sum;k.mean=(k.count)?(k.sum/k.count):(null);var h=c.data[f].slice().sort(),j=Math.floor(h.length/2);if(h.length%2===0){k.median=((h[j]+h[(j+1)])/2)}else{k.median=h[j]}}})}else{c.meta=e;c.log("initial meta:",c.meta)}},getDataSettings:function(){var d=this.getColumnSelections(),c=[];this.log("columnSelections:",d);c=[d.X.colIndex,d.Y.colIndex];if(this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked")){c.push(d.ID.colIndex)}var e={data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);return e},getColumnSelections:function(){var c={};this.$dataSettingsPanel.find("div.column-select select").each(function(){var d=$(this),e=parseInt(d.val(),10)-1;c[d.attr("name")]={colIndex:e,colName:d.children('[value="'+e+'"]').text()}});return c},getGraphSettings:function(){var e={},f=this.getColumnSelections();e.datapointSize=this.$chartSettingsPanel.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");e.width=this.$chartSettingsPanel.find("#width.numeric-slider-input").find(".slider").slider("value");e.height=this.$chartSettingsPanel.find("#height.numeric-slider-input").find(".slider").slider("value");var d=this.$chartSettingsPanel.find("input#X-axis-label").val(),c=this.$chartSettingsPanel.find("input#Y-axis-label").val();e.xLabel=(d==="X")?(f.X.colName):(d);e.yLabel=(c==="Y")?(f.Y.colName):(c);e.animDuration=10;if(this.$chartSettingsPanel.find("#animDuration.checkbox-input").is(":checked")){e.animDuration=500}this.log("graphSettings:",e);return e},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});b.templates={form:Handlebars.templates["template-visualization-scatterplotControlForm"],statsTable:Handlebars.templates["template-visualization-statsTable"],chartSettings:Handlebars.templates["template-visualization-chartSettings"]};return{LazyDataLoader:LazyDataLoader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -73,82 +73,72 @@ function program12(depth0,data) { + var buffer = "", stack1, foundHelper; + buffer += "\n "; + foundHelper = helpers.warningmessagesmall; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } + else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(13, program13, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += "\n "; + return buffer;} +function program13(depth0,data) { - return "Refresh this display";} - + var stack1, foundHelper; + foundHelper = helpers.local; + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } + if(stack1 || stack1 === 0) { return stack1; } + else { return ''; }} function program14(depth0,data) { - return "Click to see more actions for this history";} + return "You are currently viewing a deleted history!";} function program16(depth0,data) { var buffer = "", stack1, foundHelper; - buffer += "\n "; - foundHelper = helpers.warningmessagesmall; + buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>"; + foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); } - else { stack1 = depth0.warningmessagesmall; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.warningmessagesmall) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); } + else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(17, program17, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer;} -function program17(depth0,data) { - - var stack1, foundHelper; + buffer += ":</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>"; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(18, program18, data)}); } - if(stack1 || stack1 === 0) { return stack1; } - else { return ''; }} -function program18(depth0,data) { - - - return "You are currently viewing a deleted history!";} - -function program20(depth0,data) { - - var buffer = "", stack1, foundHelper; - buffer += "\n <div id=\"history-tag-annotation\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <strong>"; + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(19, program19, data)}); } + if(stack1 || stack1 === 0) { buffer += stack1; } + buffer += ":</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\"\n title=\""; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(21, program21, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>"; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(23, program23, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(23, program23, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\"\n title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(25, program25, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(25, program25, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\">\n "; stack1 = depth0.annotation; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(29, program29, data),fn:self.program(27, program27, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(25, program25, data),fn:self.program(23, program23, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n </div>\n </div>\n </div>\n "; return buffer;} -function program21(depth0,data) { +function program17(depth0,data) { return "Tags";} -function program23(depth0,data) { +function program19(depth0,data) { return "Annotation";} -function program25(depth0,data) { +function program21(depth0,data) { return "Click to edit annotation";} -function program27(depth0,data) { +function program23(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n "; @@ -158,23 +148,23 @@ buffer += escapeExpression(stack1) + "\n "; return buffer;} -function program29(depth0,data) { +function program25(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <em>"; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(30, program30, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(26, program26, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(30, program30, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(26, program26, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "</em>\n "; return buffer;} -function program30(depth0,data) { +function program26(depth0,data) { return "Describe or add notes to history";} -function program32(depth0,data) { +function program28(depth0,data) { var buffer = "", stack1, foundHelper; buffer += "\n <div id=\"message-container\">\n <div class=\""; @@ -188,12 +178,12 @@ buffer += escapeExpression(stack1) + "\n </div><br />\n </div>\n "; return buffer;} -function program34(depth0,data) { +function program30(depth0,data) { return "You are over your disk quota.\n Tool execution is on hold until your disk usage drops below your allocated quota.";} -function program36(depth0,data) { +function program32(depth0,data) { return "Your history is empty. Click 'Get Data' on the left pane to start";} @@ -214,38 +204,26 @@ stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(7, program7, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n <a id=\"history-refresh\" class=\"tooltip\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); } + buffer += "\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n\n "; + stack1 = depth0.deleted; + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(12, program12, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n href=\"javascript:void(0);\">\n <span class=\"ficon refresh large\"></span>\n </a>\n <a id=\"history-action-popup\" class=\"tooltip\" title=\""; - foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(14, program14, data)}); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n href=\"javascript:void(0);\">\n <span class=\"ficon cogs large\"></span>\n </a>\n </div>\n <div style=\"clear: both;\"></div>\n </div>\n\n "; - stack1 = depth0.deleted; + buffer += "\n\n "; + buffer += "\n "; + buffer += "\n "; + stack1 = depth0.user; + stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(16, program16, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n "; - buffer += "\n "; - buffer += "\n "; - stack1 = depth0.user; - stack1 = stack1 == null || stack1 === false ? stack1 : stack1.email; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(20, program20, data)}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; stack1 = depth0.message; - stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(32, program32, data)}); + stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(28, program28, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div id=\"quota-message-container\" style=\"display: none\">\n <div id=\"quota-message\" class=\"errormessage\">\n "; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(34, program34, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(30, program30, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(34, program34, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(30, program30, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n </div>\n </div>\n</div>\n\n<div id=\""; foundHelper = helpers.id; @@ -253,9 +231,9 @@ else { stack1 = depth0.id; stack1 = typeof stack1 === functionType ? stack1() : stack1; } buffer += escapeExpression(stack1) + "-datasets\" class=\"history-datasets-list\"></div>\n\n<div class=\"infomessagesmall\" id=\"emptyHistoryMessage\" style=\"display: none;\">\n "; foundHelper = helpers.local; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } + if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(32, program32, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(36, program36, data)}); } + if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(32, program32, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n</div>"; return buffer;}); diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js --- a/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js +++ b/static/scripts/templates/compiled/template-visualization-scatterplotControlForm.js @@ -46,7 +46,7 @@ buffer += escapeExpression(stack1) + "</option>\n "; return buffer;} - buffer += "\n\n<ul class=\"nav nav-tabs\">\n <li class=\"active\">\n <a data-toggle=\"tab\" href=\"#data-settings\">Data Controls</a>\n </li>\n <li><a data-toggle=\"tab\" href=\"#chart-settings\">Plot Controls</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart-stats\">Statistics</a></li>\n</ul>\n\n"; + buffer += "\n\n<ul class=\"nav nav-tabs\">\n <li class=\"active\"><a data-toggle=\"tab\" href=\"#data-settings\">Data Controls</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart-settings\">Plot Controls</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart-stats\">Statistics</a></li>\n <li><a data-toggle=\"tab\" href=\"#chart\">Chart</a></li>\n</ul>\n\n"; buffer += "\n<div class=\"tab-content\">\n<div id=\"data-settings\" class=\"tab-pane active\">\n\n <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 "; buffer += "\n <div class=\"column-select\">\n <label for=\"X-select\">Data column for X: </label>\n <select name=\"X\" id=\"X-select\">\n "; stack1 = depth0.numericColumns; diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -28,14 +28,6 @@ <a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a> {{/if}} - <a id="history-refresh" class="tooltip" title="{{#local}}Refresh this display{{/local}}" - href="javascript:void(0);"> - <span class="ficon refresh large"></span> - </a> - <a id="history-action-popup" class="tooltip" title="{{#local}}Click to see more actions for this history{{/local}}" - href="javascript:void(0);"> - <span class="ficon cogs large"></span> - </a></div><div style="clear: both;"></div></div> diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -378,8 +378,9 @@ quotaMeter.update() }, quotaMeter ); - - if( !Galaxy.currHistoryPanel ){ Galaxy.currHistoryPanel = historyPanel; } + // set it up to be accessible across iframes + //TODO:?? mem leak + top.Galaxy.currHistoryPanel = historyPanel; return; }); @@ -413,7 +414,7 @@ #history-name { word-wrap: break-word; font-weight: bold; - color: black; + /*color: gray;*/ } .editable-text { border: solid transparent 1px; @@ -422,7 +423,7 @@ width: 90%; margin: -2px 0px -3px -4px; font-weight: bold; - color: black; + /*color: gray;*/ } #quota-message-container { diff -r 43e41e09206d2ddc52f4a46114303ef9fd067251 -r 8481560e2c3287a75f85e3a05e59b50b18bcd634 templates/root/index.mako --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -40,11 +40,17 @@ "${_("Resume Paused Jobs")}": function() { galaxy_history.location = "${h.url_for( controller='history', action='resume_paused_jobs', current=True)}"; }, - "${_("Show Deleted Datasets")}": function() { - galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; + "${_("Collapse Expanded Datasets")}": function() { + Galaxy.currHistoryPanel.collapseAllHdaBodies(); + //galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; }, - "${_("Show Hidden Datasets")}": function() { - galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}"; + "${_("Show/Hide Deleted Datasets")}": function() { + Galaxy.currHistoryPanel.toggleShowDeleted(); + //galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; + }, + "${_("Show/Hide Hidden Datasets")}": function() { + Galaxy.currHistoryPanel.toggleShowHidden(); + //galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}"; }, "${_("Unhide Hidden Datasets")}": function() { if ( confirm( "Really unhide all hidden datasets?" ) ) { @@ -136,7 +142,14 @@ <div class="unified-panel-header" unselectable="on"><div class="unified-panel-header-inner"><div style="float: right"> - <a id="history-options-button" class='panel-header-button' href="${h.url_for( controller='root', action='history_options' )}" target="galaxy_main"><span class="ficon large cog"></span></a> + <a id="history-refresh-button" class='panel-header-button' + href="${h.url_for( controller='root', action='history' )}" target="galaxy_history"> + <span class="ficon large refresh"></span> + </a> + <a id="history-options-button" class='panel-header-button' + href="${h.url_for( controller='root', action='history_options' )}" target="galaxy_main"> + <span class="ficon large cog"></span> + </a></div><div class="panel-header-text">${_('History')}</div></div> 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: greg: More shed_util refactoring.
by Bitbucket 21 Nov '12

21 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/43e41e09206d/ changeset: 43e41e09206d user: greg date: 2012-11-21 16:50:52 summary: More shed_util refactoring. affected #: 2 files diff -r 5376431b78bf67afc967eb7dbebde50a02e69518 -r 43e41e09206d2ddc52f4a46114303ef9fd067251 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -168,16 +168,6 @@ os.close( fd ) shutil.move( filename, os.path.abspath( config_filename ) ) os.chmod( config_filename, 0644 ) -def copy_disk_sample_files_to_dir( trans, repo_files_dir, dest_path ): - sample_files = [] - for root, dirs, files in os.walk( repo_files_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name.endswith( '.sample' ): - relative_path = os.path.join( root, name ) - copy_sample_file( trans.app, relative_path, dest_path=dest_path ) - sample_files.append( name ) - return sample_files def clean_tool_shed_url( tool_shed_url ): if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. @@ -544,17 +534,6 @@ if converter_path and display_path: break return converter_path, display_path -def get_ctx_file_path_from_manifest( filename, repo, changeset_revision ): - """Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision.""" - stripped_filename = strip_path( filename ) - for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): - manifest_changeset_revision = str( repo.changectx( changeset ) ) - manifest_ctx = repo.changectx( changeset ) - for ctx_file in manifest_ctx.files(): - ctx_file_name = strip_path( ctx_file ) - if ctx_file_name == stripped_filename: - return manifest_ctx, ctx_file - return None, None def get_ctx_rev( tool_shed_url, name, owner, changeset_revision ): url = url_join( tool_shed_url, 'repository/get_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) ) response = urllib2.urlopen( url ) @@ -564,38 +543,6 @@ def get_installed_tool_shed_repository( trans, id ): """Get a repository on the Galaxy side from the database via id""" return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) -def get_list_of_copied_sample_files( repo, ctx, dir ): - """ - Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy - each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later - changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in - order to load the tools and generate metadata for them. - """ - deleted_sample_files = [] - sample_files = [] - for changeset in reversed_upper_bounded_changelog( repo, ctx ): - changeset_ctx = repo.changectx( changeset ) - for ctx_file in changeset_ctx.files(): - ctx_file_name = strip_path( ctx_file ) - # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement. - # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: - if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: - fctx = get_file_context_from_ctx( changeset_ctx, ctx_file ) - if fctx in [ 'DELETED' ]: - # Since the possibly future used if statement above is commented out, the same file that was initially added will be - # discovered in an earlier changeset in the change log and fall through to the else block below. In other words, if - # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset - # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below. In this - # way, the file contents will always be found for future tools even though the file was deleted. - if ctx_file_name not in deleted_sample_files: - deleted_sample_files.append( ctx_file_name ) - else: - sample_files.append( ctx_file_name ) - tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) ) - fh = open( tmp_ctx_file_name, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return sample_files, deleted_sample_files def get_repository_owner( cleaned_repository_url ): items = cleaned_repository_url.split( 'repos' ) repo_path = items[ 1 ] @@ -916,31 +863,6 @@ def load_installed_display_applications( app, installed_repository_dict, deactivate=False ): # Load or deactivate proprietary datatype display applications app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate ) -def load_tool_from_tmp_config( trans, repo, ctx, ctx_file, work_dir ): - tool = None - message = '' - tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) - if tmp_tool_config: - element_tree = util.parse_xml( tmp_tool_config ) - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. - tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) - if tmp_code_file_name: - tmp_code_files.append( tmp_code_file_name ) - tool, valid, message = load_tool_from_config( trans.app, tmp_tool_config ) - for tmp_code_file in tmp_code_files: - try: - os.unlink( tmp_code_file ) - except: - pass - try: - os.unlink( tmp_tool_config ) - except: - pass - return tool, message def panel_entry_per_tool( tool_section_dict ): # Return True if tool_section_dict looks like this. # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} diff -r 5376431b78bf67afc967eb7dbebde50a02e69518 -r 43e41e09206d2ddc52f4a46114303ef9fd067251 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -284,6 +284,28 @@ else: message = '' return message +def copy_disk_sample_files_to_dir( trans, repo_files_dir, dest_path ): + sample_files = [] + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + relative_path = os.path.join( root, name ) + copy_sample_file( trans.app, relative_path, dest_path=dest_path ) + sample_files.append( name ) + return sample_files +def copy_file_from_manifest( repo, ctx, filename, dir ): + """Copy the latest version of the file named filename from the repository manifest to the directory to which dir refers.""" + for changeset in reversed_upper_bounded_changelog( repo, ctx ): + changeset_ctx = repo.changectx( changeset ) + fctx = get_file_context_from_ctx( changeset_ctx, filename ) + if fctx and fctx not in [ 'DELETED' ]: + file_path = os.path.join( dir, filename ) + fh = open( file_path, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return file_path + return None def copy_sample_file( app, filename, dest_path=None ): """Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path is ~/tool-data.""" if dest_path is None: @@ -603,10 +625,12 @@ is_valid = False if is_valid: for repository_elem in root.findall( 'repository' ): - repository_dependencies_tups.append( ( repository_elem.attrib[ 'toolshed' ], - repository_elem.attrib[ 'name' ], - repository_elem.attrib[ 'owner'], - repository_elem.attrib[ 'changeset_revision' ] ) ) + repository_dependencies_tup = ( repository_elem.attrib[ 'toolshed' ], + repository_elem.attrib[ 'name' ], + repository_elem.attrib[ 'owner'], + repository_elem.attrib[ 'changeset_revision' ] ) + if repository_dependencies_tup not in repository_dependencies_tups: + repository_dependencies_tups.append( repository_dependencies_tup ) if repository_dependencies_tups: metadata_dict[ 'repository_dependencies' ] = repository_dependencies_tups return metadata_dict @@ -723,6 +747,17 @@ # quiet = True _ui.setconfig( 'ui', 'quiet', True ) return _ui +def get_ctx_file_path_from_manifest( filename, repo, changeset_revision ): + """Get the ctx file path for the latest revision of filename from the repository manifest up to the value of changeset_revision.""" + stripped_filename = strip_path( filename ) + for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): + manifest_changeset_revision = str( repo.changectx( changeset ) ) + manifest_ctx = repo.changectx( changeset ) + for ctx_file in manifest_ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if ctx_file_name == stripped_filename: + return manifest_ctx, ctx_file + return None, None def get_file_context_from_ctx( ctx, filename ): # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to @@ -743,6 +778,77 @@ if deleted: return 'DELETED' return None +def get_list_of_copied_sample_files( repo, ctx, dir ): + """ + Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy + each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later + changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in + order to load the tools and generate metadata for them. + """ + deleted_sample_files = [] + sample_files = [] + for changeset in reversed_upper_bounded_changelog( repo, ctx ): + changeset_ctx = repo.changectx( changeset ) + for ctx_file in changeset_ctx.files(): + ctx_file_name = strip_path( ctx_file ) + # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement. + # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: + if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: + fctx = get_file_context_from_ctx( changeset_ctx, ctx_file ) + if fctx in [ 'DELETED' ]: + # Since the possibly future used if statement above is commented out, the same file that was initially added will be + # discovered in an earlier changeset in the change log and fall through to the else block below. In other words, if + # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset + # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below. In this + # way, the file contents will always be found for future tools even though the file was deleted. + if ctx_file_name not in deleted_sample_files: + deleted_sample_files.append( ctx_file_name ) + else: + sample_files.append( ctx_file_name ) + tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) ) + fh = open( tmp_ctx_file_name, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return sample_files, deleted_sample_files +def get_named_tmpfile_from_ctx( ctx, filename, dir ): + filename = strip_path( filename ) + for ctx_file in ctx.files(): + ctx_file_name = strip_path( ctx_file ) + if filename == ctx_file_name: + try: + # If the file was moved, its destination file contents will be returned here. + fctx = ctx[ ctx_file ] + except LookupError, e: + # Continue looking in case the file was moved. + fctx = None + continue + if fctx: + fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return tmp_filename + return None +def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ): + parent_id = None + # Compare from most recent to oldest. + changeset_revisions.reverse() + for changeset_revision in changeset_revisions: + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + metadata = repository_metadata.metadata + tools_dicts = metadata.get( 'tools', [] ) + for tool_dict in tools_dicts: + if tool_dict[ 'guid' ] == guid: + # The tool has not changed between the compared changeset revisions. + continue + if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version: + # The tool version is different, so we've found the parent. + return tool_dict[ 'guid' ] + if parent_id is None: + # The tool did not change through all of the changeset revisions. + return old_id def get_readme_file_names( repository_name ): readme_files = [ 'readme', 'read_me', 'install' ] valid_filenames = [ r for r in readme_files ] @@ -803,27 +909,20 @@ elif all_metadata_records: return all_metadata_records[ 0 ] return None -def get_named_tmpfile_from_ctx( ctx, filename, dir ): - filename = strip_path( filename ) - for ctx_file in ctx.files(): - ctx_file_name = strip_path( ctx_file ) - if filename == ctx_file_name: - try: - # If the file was moved, its destination file contents will be returned here. - fctx = ctx[ ctx_file ] - except LookupError, e: - # Continue looking in case the file was moved. - fctx = None - continue - if fctx: - fh = tempfile.NamedTemporaryFile( 'wb', dir=dir ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return tmp_filename - return None +def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ): + if resetting_all_metadata_on_repository: + full_path_to_file = os.path.join( root, name ) + stripped_path_to_file = full_path_to_file.replace( work_dir, '' ) + if stripped_path_to_file.startswith( '/' ): + stripped_path_to_file = stripped_path_to_file[ 1: ] + relative_path_to_file = os.path.join( relative_install_dir, stripped_path_to_file ) + else: + relative_path_to_file = os.path.join( root, name ) + if relative_install_dir and \ + shed_config_dict.get( 'tool_path' ) and \ + relative_path_to_file.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ): + relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] + return relative_path_to_file def get_sample_files_from_disk( repository_files_dir, tool_path = None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): if resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip it when setting metadata. @@ -852,38 +951,6 @@ relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths -def get_parent_id( trans, id, old_id, version, guid, changeset_revisions ): - parent_id = None - # Compare from most recent to oldest. - changeset_revisions.reverse() - for changeset_revision in changeset_revisions: - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - metadata = repository_metadata.metadata - tools_dicts = metadata.get( 'tools', [] ) - for tool_dict in tools_dicts: - if tool_dict[ 'guid' ] == guid: - # The tool has not changed between the compared changeset revisions. - continue - if tool_dict[ 'id' ] == old_id and tool_dict[ 'version' ] != version: - # The tool version is different, so we've found the parent. - return tool_dict[ 'guid' ] - if parent_id is None: - # The tool did not change through all of the changeset revisions. - return old_id -def get_relative_path_to_repository_file( root, name, relative_install_dir, work_dir, shed_config_dict, resetting_all_metadata_on_repository ): - if resetting_all_metadata_on_repository: - full_path_to_file = os.path.join( root, name ) - stripped_path_to_file = full_path_to_file.replace( work_dir, '' ) - if stripped_path_to_file.startswith( '/' ): - stripped_path_to_file = stripped_path_to_file[ 1: ] - relative_path_to_file = os.path.join( relative_install_dir, stripped_path_to_file ) - else: - relative_path_to_file = os.path.join( root, name ) - if relative_install_dir and \ - shed_config_dict.get( 'tool_path' ) and \ - relative_path_to_file.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ): - relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] - return relative_path_to_file def handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_dependency_dict, new_dependency_dict ): """ This method is called when a Galaxy admin is getting updates for an installed tool shed repository in order to cover the case where an @@ -969,6 +1036,31 @@ valid = False error_message = str( e ) return tool, valid, error_message +def load_tool_from_tmp_config( trans, repo, ctx, ctx_file, work_dir ): + tool = None + message = '' + tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) + if tmp_tool_config: + element_tree = util.parse_xml( tmp_tool_config ) + element_tree_root = element_tree.getroot() + # Look for code files required by the tool config. + tmp_code_files = [] + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + tmp_code_file_name = copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + if tmp_code_file_name: + tmp_code_files.append( tmp_code_file_name ) + tool, valid, message = load_tool_from_config( trans.app, tmp_tool_config ) + for tmp_code_file in tmp_code_files: + try: + os.unlink( tmp_code_file ) + except: + pass + try: + os.unlink( tmp_tool_config ) + except: + pass + return tool, message def open_repository_files_folder( trans, folder_path ): try: files_list = get_repository_files( trans, folder_path ) 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: jgoecks: eXpress in tool menus: (a) move to position after Cuff* tools and (b) add to main's tool conf.
by Bitbucket 21 Nov '12

21 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5376431b78bf/ changeset: 5376431b78bf user: jgoecks date: 2012-11-21 15:56:01 summary: eXpress in tool menus: (a) move to position after Cuff* tools and (b) add to main's tool conf. affected #: 2 files diff -r 46339150e5e134fb2eb57e4945617841e03a5a3f -r 5376431b78bf67afc967eb7dbebde50a02e69518 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -330,8 +330,9 @@ <tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /> - <tool file="ngs_rna/cuffmerge_wrapper.xml" /> + <tool file="ngs_rna/cuffmerge_wrapper.xml" /><tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <tool file="ngs_rna/express_wrapper.xml" /><label text="Filtering" id="filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /></section> diff -r 46339150e5e134fb2eb57e4945617841e03a5a3f -r 5376431b78bf67afc967eb7dbebde50a02e69518 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -331,9 +331,9 @@ <tool file="ngs_rna/tophat_color_wrapper.xml" /><tool file="ngs_rna/cufflinks_wrapper.xml" /><tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffmerge_wrapper.xml" /> + <tool file="ngs_rna/cuffdiff_wrapper.xml" /><tool file="ngs_rna/express_wrapper.xml" /> - <tool file="ngs_rna/cuffmerge_wrapper.xml" /> - <tool file="ngs_rna/cuffdiff_wrapper.xml" /><!-- Trinity is very memory-intensive and should only be enabled/run on instances with sufficient resources. <label text="De novo Assembly" id="de_novo_assembly "/> 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: fix column selection broken in 7002f41
by Bitbucket 20 Nov '12

20 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/46339150e5e1/ changeset: 46339150e5e1 user: carlfeberhard date: 2012-11-20 21:42:01 summary: scatterplot: fix column selection broken in 7002f41 affected #: 1 file diff -r 7002f41bcaa3b1a5f5023e3c2d523488812873df -r 46339150e5e134fb2eb57e4945617841e03a5a3f static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -939,7 +939,7 @@ var selections = {}; this.$dataSettingsPanel.find( 'div.column-select select' ).each( function(){ var $this = $( this ), - val = $this.val(); + val = parseInt( $this.val(), 10 ) - 1; selections[ $this.attr( 'name' ) ] = { colIndex : val, colName : $this.children( '[value="' + val + '"]' ).text() 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 Bitbucket 20 Nov '12

20 Nov '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0941c74d1d05/ changeset: 0941c74d1d05 user: carlfeberhard date: 2012-11-20 21:30:22 summary: scatterplot: add ability to auto-render based on query string affected #: 4 files diff -r 67b9614dcab440027292c5dc387ef2eb1a763c19 -r 0941c74d1d058ad6183347417e45fd5fd1528501 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -786,6 +786,9 @@ @web.expose def scatterplot( self, trans, dataset_id, **kwargs ): + """ + Returns a page that controls and renders a scatteplot graph. + """ # Get HDA. hda = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) hda_dict = hda.get_api_value() @@ -793,6 +796,7 @@ if( hda_dict[ 'metadata_column_names' ] == None and hasattr( hda.datatype, 'column_names' ) ): hda_dict[ 'metadata_column_names' ] = hda.datatype.column_names + history_id = trans.security.encode_id( hda.history.id ) #TODO: add column data @@ -845,4 +849,3 @@ name = fields[4] rows.append( [location, name] ) return { 'data': rows } - diff -r 67b9614dcab440027292c5dc387ef2eb1a763c19 -r 0941c74d1d058ad6183347417e45fd5fd1528501 static/scripts/templates/visualization-templates.html --- a/static/scripts/templates/visualization-templates.html +++ b/static/scripts/templates/visualization-templates.html @@ -2,11 +2,10 @@ {{! main controls }} <ul class="nav nav-tabs"> - <li class="active"> - <a data-toggle="tab" href="#data-settings">Data Controls</a> - </li> + <li class="active"><a data-toggle="tab" href="#data-settings">Data Controls</a></li><li><a data-toggle="tab" href="#chart-settings">Plot Controls</a></li><li><a data-toggle="tab" href="#chart-stats">Statistics</a></li> + <li><a data-toggle="tab" href="#chart">Chart</a></li></ul> {{! data settings }} diff -r 67b9614dcab440027292c5dc387ef2eb1a763c19 -r 0941c74d1d058ad6183347417e45fd5fd1528501 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -412,14 +412,14 @@ } // titles - newDatapoints.attr( 'title', function( d, i ){ - return (( ids )?( ids[ i ] + ': ' ):( '' )) + newXCol[ i ] + ', ' + newYCol[ i ]; - }); + //newDatapoints.attr( 'title', function( d, i ){ + // return (( ids )?( ids[ i ] + ': ' ):( '' )) + newXCol[ i ] + ', ' + newYCol[ i ]; + //}); // events newDatapoints //TODO: remove magic numbers - .on( 'mouseover', function(){ + .on( 'mouseover', function( d, i ){ var datapoint = d3.select( this ); datapoint .style( 'fill', 'red' ) @@ -438,12 +438,24 @@ .attr( 'x1', datapoint.attr( 'cx' ) ).attr( 'y1', datapoint.attr( 'cy' ) ) .attr( 'x2', datapoint.attr( 'cx' ) ).attr( 'y2', plot.config.height ) .classed( 'hoverline', true ); + + //var datapointWindowPos = $( this ).position(); + var datapointWindowPos = $( this ).offset(); + window.dot = this; + console.debug( 'datapointWindowPos:', datapointWindowPos ); + console.debug( 'datapoint r:', datapoint.attr( 'r' ) ); + //this.popup = make_abs_box( datapointWindowPos.top, datapointWindowPos.left + datapoint.attr( 'r' ), + this.popup = make_abs_box( datapointWindowPos.top, datapointWindowPos.left, + newXCol[ i ], newYCol[ i ], ( ids )?( ids[ i ] ):( undefined ) ); + $( 'body' ).append( this.popup ); }) .on( 'mouseout', function(){ d3.select( this ) .style( 'fill', 'black' ) .style( 'fill-opacity', 0.2 ); - + if( this.popup ){ + this.popup.remove(); + } d3.selectAll( '.hoverline' ).remove(); }); @@ -499,7 +511,7 @@ loadingIndicatorImage : 'loading_large_white_bg.gif', initialize : function( attributes ){ - if( this.logger ){ window.form = this; } + console.debug( this + '.initialize, attributes:', attributes ); this.dataset = null; this.chartConfig = null; @@ -517,7 +529,7 @@ }, initializeFromAttributes : function( attributes ){ - // ensure certain vars we need are passed in attributes + // required settings: ensure certain vars we need are passed in attributes if( !attributes || !attributes.dataset ){ throw( "ScatterplotView requires a dataset" ); } else { @@ -586,9 +598,9 @@ loadingIndicatorImagePath : galaxy_paths.get( 'image_path' ) + '/' + this.loadingIndicatorImage }; + //TODO: isNumericColumn // gather column indeces (from metadata_column_types) and names (from metadata_columnnames) _.each( this.dataset.metadata_column_types, function( type, index ){ - //TODO: using 0-based indeces // label with the name if available (fall back on 'column <index>') var name = 'column ' + ( index + 1 ); if( view.dataset.metadata_column_names ){ @@ -597,23 +609,46 @@ // filter numeric columns to their own list if( type === 'int' || type === 'float' ){ - formData.numericColumns.push({ index: index, name: name }); + formData.numericColumns.push({ index: ( index + 1 ), name: name }); } - formData.allColumns.push({ index: index, name: name }); + formData.allColumns.push({ index: ( index + 1 ), name: name }); }); - //TODO: other vals: max_vals, start_val, pagination (plot-settings) // render template and set up panels, store refs this.$el.append( ScatterplotControlForm.templates.form( formData ) ); + this.$dataSettingsPanel = this.$el.find( '.tab-pane#data-settings' ); this.$chartSettingsPanel = this._render_chartSettings(); this.$statsPanel = this.$el.find( '.tab-pane#chart-stats' ); - + + // preset to column selectors if they were passed in the config + this.$dataSettingsPanel.find( '#X-select' ).val( this.chartConfig.xColumn ); + this.$dataSettingsPanel.find( '#Y-select' ).val( this.chartConfig.yColumn ); + if( this.chartConfig.idColumn !== undefined ){ + this.$dataSettingsPanel.find( '#include-id-checkbox' ) + .attr( 'checked', true ).trigger( 'change' ); + this.$dataSettingsPanel.find( '#ID-select' ).val( this.chartConfig.idColumn ); + } + //this.$el.find( 'ul.nav' ).find( 'a[href="#chart-settings"]' ).tab( 'show' ); + + //TODO:?? add autoRender=1 to query maybe? + if( this.chartConfig.xColumn && this.chartConfig.yColumn ){ + this.renderPlot(); + } return this; }, - + + //TODO: seems like a function of dataset or metadata + isColumnNumeric : function( index ){ + if( ( index >= 0 ) && ( index < this.dataset.metadata_column_types.length ) ){ + var columnType = this.dataset.metadata_column_types[ index ]; + return ( columnType === 'int' || columnType === 'float' ); + } + return false; + }, + _render_chartSettings : function(){ // chart settings panel var chartControl = this, @@ -658,7 +693,7 @@ // ------------------------------------------------------------------------- EVENTS events : { - 'click #include-id-checkbox' : 'toggleThirdColumnSelector', + 'change #include-id-checkbox' : 'toggleThirdColumnSelector', 'click #data-settings #render-button' : 'renderPlot', 'click #chart-settings #render-button' : 'changeChartSettings' }, @@ -948,7 +983,7 @@ }, toString : function(){ - return 'ScatterplotControlForm(' + this.dataset.id + ')'; + return 'ScatterplotControlForm(' + (( this.dataset )?( this.dataset.id ):( '' )) + ')'; } }); diff -r 67b9614dcab440027292c5dc387ef2eb1a763c19 -r 0941c74d1d058ad6183347417e45fd5fd1528501 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -193,6 +193,15 @@ fill-opacity: 0.2; } +/* -------------------------------------------- info box */ +.zero-dimensions { + width: 0; + height: 0; + border-top: 8px solid transparent; + border-bottom: 8px solid transparent; + border-right: 8px solid grey; +} + </style></%def> @@ -207,21 +216,88 @@ require([ "viz/scatterplot" ], function( scatterplot ){ var hda = ${h.to_json_string( hda )}, - historyID = '${historyID}'; - - settingsForm = new scatterplot.ScatterplotControlForm({ - dataset : hda, - el : $( '#chart-settings-form' ), - apiDatasetsURL : "${h.url_for( controller='/api/datasets' )}", + historyID = '${historyID}', + querySettings = ${h.to_json_string( kwargs )}, + chartConfig = _.extend( querySettings, { + containerSelector : '#chart-holder', + //TODO: move to ScatterplotControlForm.initialize + marginTop : ( querySettings.marginTop > 20 )?( querySettings.marginTop ):( 20 ), - chartConfig : { - containerSelector : '#chart-holder', - marginTop : 20, - } + xColumn : querySettings.xColumn, + yColumn : querySettings.yColumn, + idColumn : querySettings.idColumn + }); + console.debug( querySettings ); + + var settingsForm = new scatterplot.ScatterplotControlForm({ + dataset : hda, + apiDatasetsURL : "${h.url_for( controller='/api/datasets' )}", + el : $( '#chart-settings-form' ), + chartConfig : chartConfig }).render(); }); + +function make_abs_box( top, left, x, y, id ){ + console.debug( top, left, x, y, id ); + var ARROW_SIZE = 8, + ARROW_COLOR = 'grey', + DIST_TO_POINT = 4, + halfArrowSize = ARROW_SIZE / 2; + + var boxContainer = $( '<div />' ) + .attr( 'id', 'abs-box-container' ) + // top left arrow + .css({ + 'position' : 'absolute', + 'top' : top - halfArrowSize, + 'left' : left + ARROW_SIZE + DIST_TO_POINT, + 'background-color': 'transparent', + }); + window.boxContainer = boxContainer; + + var arrowLeft = $( '<div />' ) + .attr( 'id', 'abs-box-arrow' ) + .addClass( 'zero-dimensions' ) + .css({ + 'border-top' : ARROW_SIZE + 'px solid transparent', + 'border-bottom' : ARROW_SIZE + 'px solid transparent', + 'border-right' : ARROW_SIZE + 'px solid ' + ARROW_COLOR, + }); + boxContainer.append( arrowLeft ); + window.arrow = arrowLeft; + + console.debug( 'arrow height:', arrowLeft.height() ); + var boxInfo = $( '<div />' ) + .attr( 'id', 'abs-box' ) + .css({ + 'position' : 'relative', + //TODO: 4 here is the border-radius + 'top' : -( 2 * ARROW_SIZE + 6 ), + 'left' : ARROW_SIZE, + 'border' : '2px solid grey', + 'border-radius' : '4px', + 'padding' : '4px', + 'background-color': 'white', + 'box-shadow' : '4px 4px 4px black' + }); + + // remove + if( id ){ + $( '<div />' ).addClass( 'abs-box-id' ).css( 'font-weight', 'bold' ).text( id ).appendTo( boxInfo ); + } + $( '<div />' ).addClass( 'abs-box-x' ).text( x ).appendTo( boxInfo ); + $( '<div />' ).addClass( 'abs-box-y' ).text( y ).appendTo( boxInfo ); + boxContainer.append( boxInfo ); + boxContainer.append( '<div style="clear:both"></div>' ); + window.boxInfo = boxContainer; + + //console.debug( boxContainer ); + return boxContainer; +} + + </script></%def> https://bitbucket.org/galaxy/galaxy-central/changeset/f25f13784d20/ changeset: f25f13784d20 user: carlfeberhard date: 2012-11-20 21:32:14 summary: scatterplot: clean up affected #: 2 files diff -r 0941c74d1d058ad6183347417e45fd5fd1528501 -r f25f13784d20b7f8697ff499b73339ac7d2b4acc static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -412,9 +412,9 @@ } // titles - //newDatapoints.attr( 'title', function( d, i ){ - // return (( ids )?( ids[ i ] + ': ' ):( '' )) + newXCol[ i ] + ', ' + newYCol[ i ]; - //}); + newDatapoints.attr( 'title', function( d, i ){ + return (( ids )?( ids[ i ] + ': ' ):( '' )) + newXCol[ i ] + ', ' + newYCol[ i ]; + }); // events newDatapoints @@ -440,23 +440,21 @@ .classed( 'hoverline', true ); //var datapointWindowPos = $( this ).position(); - var datapointWindowPos = $( this ).offset(); - window.dot = this; - console.debug( 'datapointWindowPos:', datapointWindowPos ); - console.debug( 'datapoint r:', datapoint.attr( 'r' ) ); - //this.popup = make_abs_box( datapointWindowPos.top, datapointWindowPos.left + datapoint.attr( 'r' ), - this.popup = make_abs_box( datapointWindowPos.top, datapointWindowPos.left, - newXCol[ i ], newYCol[ i ], ( ids )?( ids[ i ] ):( undefined ) ); - $( 'body' ).append( this.popup ); + //var datapointWindowPos = $( this ).offset(); + //window.dot = this; + ////this.popup = make_abs_box( datapointWindowPos.top, datapointWindowPos.left + datapoint.attr( 'r' ), + //this.popup = make_abs_box( datapointWindowPos.top, datapointWindowPos.left, + // newXCol[ i ], newYCol[ i ], ( ids )?( ids[ i ] ):( undefined ) ); + //$( 'body' ).append( this.popup ); }) .on( 'mouseout', function(){ d3.select( this ) .style( 'fill', 'black' ) .style( 'fill-opacity', 0.2 ); - if( this.popup ){ - this.popup.remove(); - } d3.selectAll( '.hoverline' ).remove(); + //if( this.popup ){ + // this.popup.remove(); + //} }); return newDatapoints; @@ -511,7 +509,7 @@ loadingIndicatorImage : 'loading_large_white_bg.gif', initialize : function( attributes ){ - console.debug( this + '.initialize, attributes:', attributes ); + this.log( this + '.initialize, attributes:', attributes ); this.dataset = null; this.chartConfig = null; diff -r 0941c74d1d058ad6183347417e45fd5fd1528501 -r f25f13784d20b7f8697ff499b73339ac7d2b4acc templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -227,7 +227,7 @@ yColumn : querySettings.yColumn, idColumn : querySettings.idColumn }); - console.debug( querySettings ); + //console.debug( querySettings ); var settingsForm = new scatterplot.ScatterplotControlForm({ dataset : hda, https://bitbucket.org/galaxy/galaxy-central/changeset/7002f41bcaa3/ changeset: 7002f41bcaa3 user: carlfeberhard date: 2012-11-20 21:32:40 summary: pack scripts affected #: 1 file diff -r f25f13784d20b7f8697ff499b73339ac7d2b4acc -r 7002f41bcaa3b1a5f5023e3c2d523488812873df static/scripts/packed/viz/scatterplot.js --- a/static/scripts/packed/viz/scatterplot.js +++ b/static/scripts/packed/viz/scatterplot.js @@ -1,1 +1,1 @@ -define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","../templates/compiled/template-visualization-scatterplotControlForm","../templates/compiled/template-visualization-statsTable","../templates/compiled/template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../libs/jquery/jquery-ui"],function(){function a(f){var d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(console,i)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(i,j){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart");this.content=this.svg.append("svg:g").attr("class","content").attr("id",this.config.id);this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.adjustChartDimensions=function(l,j,i,k){l=l||0;j=j||0;i=i||0;k=k||0;this.svg.attr("width",this.config.width+(this.config.marginRight+j)+(this.config.marginLeft+k)).attr("height",this.config.height+(this.config.marginTop+l)+(this.config.marginBottom+i)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+k,this.config.marginTop+l))};this.preprocessData=function(k,j,i){return(k.length>this.config.maxDataPoints)?(k.slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains=function(i,k,j){this.xMin=this.config.xMin||(j)?(j[0].min):(d3.min(i));this.xMax=this.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=this.config.yMin||(j)?(j[1].min):(d3.min(k));this.yMax=this.config.yMax||(j)?(j[1].max):(d3.max(k))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);var i=this.yAxis.selectAll("text").filter(function(m,l){return l!==0});this.yLongestLabel=d3.max(i[0].map(function(m,l){return(d3.select(m).text()).length}))||0;var j=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(j-g);if(this.config.marginLeft<j){var k=(j)-this.config.marginLeft;k=(k<0)?(0):(k);this.adjustChartDimensions(0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(i){};this.glyphFinalState=function(i){};this.glyphExitState=function(i){};this.renderDatapoints=function(i,l,j){this.log(this+".renderDatapoints",arguments);var k=0;this.datapoints=this.addDatapoints(i,l,j,".glyph");this.datapoints.exit().each(function(){k+=1}).transition().duration(this.config.animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs removed")};this.addDatapoints=function(m,k,i,l){this.log(this+".addDatapoints",arguments);var p=this,o=0,q=function(s,r){return p.xScale(m[r])},j=function(s,r){return p.yScale(k[r])};var n=this.content.selectAll(l);this.log("existing datapoints:",n);n=n.data(m);o=0;n.enter().append("svg:circle").each(function(){o+=1}).classed("glyph",true).attr("cx",q).attr("cy",j).attr("r",0);this.log(o," new glyphs created");o=0;n.transition().duration(this.config.animDuration).each(function(){o+=1}).attr("cx",q).attr("cy",j).attr("r",p.config.datapointSize);this.log(o," existing glyphs transitioned");if(i){n.attr("data",function(s,r){return(i[r])})}n.attr("title",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]});n.on("mouseover",function(){var r=d3.select(this);r.style("fill","red").style("fill-opacity",1);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",r.attr("cx")).attr("y1",r.attr("cy")).attr("x2",0).attr("y2",r.attr("cy")).classed("hoverline",true);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",r.attr("cx")).attr("y1",r.attr("cy")).attr("x2",r.attr("cx")).attr("y2",p.config.height).classed("hoverline",true)}).on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return n};this.render=function(k,l){this.log(this+".render",arguments);var i=k[0],m=k[1],j=(k.length>2)?(k[2]):(undefined);i=this.preprocessData(i);m=this.preprocessData(m);this.log("xCol len",i.length,"yCol len",m.length);this.setUpDomains(i,m,l);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,m,j)}}var b=BaseView.extend(LoggableMixin).extend({className:"scatterplot-settings-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"loading_large_white_bg.gif",initialize:function(c){if(this.logger){window.form=this}this.dataset=null;this.chartConfig=null;this.plot=null;this.loader=null;this.$statsPanel=null;this.$chartSettingsPanel=null;this.$dataSettingsPanel=null;this.dataFetch=null;this.initializeFromAttributes(c);this.initializeChart(c);this.initializeDataLoader(c)},initializeFromAttributes:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("dataset:",this.dataset);if(!c.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=c.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("this.dataURL:",this.dataURL)},initializeChart:function(c){this.chartConfig=c.chartConfig||{};if(this.logger){this.chartConfig.debugging=true}this.log("initial chartConfig:",this.chartConfig);this.plot=new a(this.chartConfig);this.chartConfig=this.plot.config},initializeDataLoader:function(d){var c=this;this.loader=new LazyDataLoader({logger:(this.logger)?(this.logger):(null),url:null,start:d.start||0,total:d.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})}});$(this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);alert("ERROR fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:function(){var c=this,d={config:this.chartConfig,allColumns:[],numericColumns:[],loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage};_.each(this.dataset.metadata_column_types,function(g,f){var e="column "+(f+1);if(c.dataset.metadata_column_names){e=c.dataset.metadata_column_names[f]}if(g==="int"||g==="float"){d.numericColumns.push({index:f,name:e})}d.allColumns.push({index:f,name:e})});this.$el.append(b.templates.form(d));this.$dataSettingsPanel=this.$el.find(".tab-pane#data-settings");this.$chartSettingsPanel=this._render_chartSettings();this.$statsPanel=this.$el.find(".tab-pane#chart-stats");return this},_render_chartSettings:function(){var c=this,d=this.$el.find(".tab-pane#chart-settings"),e={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};d.append(b.templates.chartSettings(this.chartConfig));d.find(".numeric-slider-input").each(function(){var h=$(this),g=h.find(".slider-output"),i=h.find(".slider"),j=h.attr("id");function f(){var l=$(this),k=l.slider("value");g.text(k)}i.slider(_.extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d},events:{"click #include-id-checkbox":"toggleThirdColumnSelector","click #data-settings #render-button":"renderPlot","click #chart-settings #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},showLoadingIndicator:function(d,e){d=d||"";var c=this.$el.find("div#loading-indicator");messageBox=c.find(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut("fast",function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e()}}else{if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:function(c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},renderPlot:function(){var c=this;c.data=null;c.meta=null;_.extend(this.chartConfig,this.getGraphSettings());this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("this.loader, url:",this.loader.url,"total:",this.loader.total);$(this.loader).bind("loaded.new",function(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse(d);c.log("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicator("Rendering...",function(){c.$el.find("ul.nav").find('a[href="#chart-stats"]').tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.meta);c.hideLoadingIndicator()})});$(this.loader).bind("complete",function(d,e){c.log("complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetching data...",function(){c.loader.load()})},renderStats:function(){this.$statsPanel.html(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var c=this;newGraphSettings=this.getGraphSettings();this.log("newGraphSettings:",newGraphSettings);_.extend(this.chartConfig,newGraphSettings);this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);if(c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.plot.render(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot()}},postProcessDataFetchResponse:function(c){this.postProcessData(c.data);this.postProcessMeta(c.meta)},postProcessData:function(d){var c=this;if(c.data){_.each(d,function(f,e){c.data[e]=c.data[e].concat(f)})}else{c.data=d}},postProcessMeta:function(e){var c=this,d=this.dataset.metadata_column_types;if(c.meta){_.each(e,function(g,f){var k=c.meta[f],i=d[f];c.log(f+" postprocessing meta:",g);k.count+=(g.count)?(g.count):(0);c.log(f,"count:",k.count);if((i==="int")||(i==="float")){k.min=Math.min(g.min,k.min);k.max=Math.max(g.max,k.max);k.sum=g.sum+k.sum;k.mean=(k.count)?(k.sum/k.count):(null);var h=c.data[f].slice().sort(),j=Math.floor(h.length/2);if(h.length%2===0){k.median=((h[j]+h[(j+1)])/2)}else{k.median=h[j]}}})}else{c.meta=e;c.log("initial meta:",c.meta)}},getDataSettings:function(){var d=this.getColumnSelections(),c=[];this.log("columnSelections:",d);c=[d.X.colIndex,d.Y.colIndex];if(this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked")){c.push(d.ID.colIndex)}var e={data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);return e},getColumnSelections:function(){var c={};this.$dataSettingsPanel.find("div.column-select select").each(function(){var d=$(this),e=d.val();c[d.attr("name")]={colIndex:e,colName:d.children('[value="'+e+'"]').text()}});return c},getGraphSettings:function(){var e={},f=this.getColumnSelections();e.datapointSize=this.$chartSettingsPanel.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");e.width=this.$chartSettingsPanel.find("#width.numeric-slider-input").find(".slider").slider("value");e.height=this.$chartSettingsPanel.find("#height.numeric-slider-input").find(".slider").slider("value");var d=this.$chartSettingsPanel.find("input#X-axis-label").val(),c=this.$chartSettingsPanel.find("input#Y-axis-label").val();e.xLabel=(d==="X")?(f.X.colName):(d);e.yLabel=(c==="Y")?(f.Y.colName):(c);e.animDuration=10;if(this.$chartSettingsPanel.find("#animDuration.checkbox-input").is(":checked")){e.animDuration=500}this.log("graphSettings:",e);return e},toString:function(){return"ScatterplotControlForm("+this.dataset.id+")"}});b.templates={form:Handlebars.templates["template-visualization-scatterplotControlForm"],statsTable:Handlebars.templates["template-visualization-statsTable"],chartSettings:Handlebars.templates["template-visualization-chartSettings"]};return{LazyDataLoader:LazyDataLoader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ No newline at end of file +define(["../libs/underscore","../mvc/base-mvc","../utils/LazyDataLoader","../templates/compiled/template-visualization-scatterplotControlForm","../templates/compiled/template-visualization-statsTable","../templates/compiled/template-visualization-chartSettings","../libs/d3","../libs/bootstrap","../libs/jquery/jquery-ui"],function(){function a(f){var d=10,h=7,g=10,e=8,c=5;this.log=function(){if(this.debugging&&console&&console.debug){var i=Array.prototype.slice.call(arguments);i.unshift(this.toString());console.debug.apply(console,i)}};this.log("new TwoVarScatterplot:",f);this.defaults={id:"TwoVarScatterplot",containerSelector:"body",maxDataPoints:30000,datapointSize:4,animDuration:500,xNumTicks:10,yNumTicks:10,xAxisLabelBumpY:40,yAxisLabelBumpX:-35,width:500,height:500,marginTop:50,marginRight:50,marginBottom:50,marginLeft:50,xMin:null,xMax:null,yMin:null,yMax:null,xLabel:"X",yLabel:"Y"};this.config=_.extend({},this.defaults,f);this.updateConfig=function(i,j){_.extend(this.config,i)};this.toString=function(){return this.config.id};this.translateStr=function(i,j){return"translate("+i+","+j+")"};this.rotateStr=function(j,i,k){return"rotate("+j+","+i+","+k+")"};this.svg=d3.select(this.config.containerSelector).append("svg:svg").attr("class","chart");this.content=this.svg.append("svg:g").attr("class","content").attr("id",this.config.id);this.xAxis=this.content.append("g").attr("class","axis").attr("id","x-axis");this.xAxisLabel=this.xAxis.append("text").attr("class","axis-label").attr("id","x-axis-label");this.yAxis=this.content.append("g").attr("class","axis").attr("id","y-axis");this.yAxisLabel=this.yAxis.append("text").attr("class","axis-label").attr("id","y-axis-label");this.adjustChartDimensions=function(l,j,i,k){l=l||0;j=j||0;i=i||0;k=k||0;this.svg.attr("width",this.config.width+(this.config.marginRight+j)+(this.config.marginLeft+k)).attr("height",this.config.height+(this.config.marginTop+l)+(this.config.marginBottom+i)).style("display","block");this.content=this.svg.select("g.content").attr("transform",this.translateStr(this.config.marginLeft+k,this.config.marginTop+l))};this.preprocessData=function(k,j,i){return(k.length>this.config.maxDataPoints)?(k.slice(0,this.config.maxDataPoints)):(k)};this.setUpDomains=function(i,k,j){this.xMin=this.config.xMin||(j)?(j[0].min):(d3.min(i));this.xMax=this.config.xMax||(j)?(j[0].max):(d3.max(i));this.yMin=this.config.yMin||(j)?(j[1].min):(d3.min(k));this.yMax=this.config.yMax||(j)?(j[1].max):(d3.max(k))};this.setUpScales=function(){this.xScale=d3.scale.linear().domain([this.xMin,this.xMax]).range([0,this.config.width]),this.yScale=d3.scale.linear().domain([this.yMin,this.yMax]).range([this.config.height,0])};this.setUpXAxis=function(){this.xAxisFn=d3.svg.axis().scale(this.xScale).ticks(this.config.xNumTicks).orient("bottom");this.xAxis.attr("transform",this.translateStr(0,this.config.height)).call(this.xAxisFn);this.xLongestLabel=d3.max(_.map([this.xMin,this.xMax],function(i){return(String(i)).length}));if(this.xLongestLabel>=c){this.xAxis.selectAll("g").filter(":nth-child(odd)").style("display","none")}this.xAxisLabel.attr("x",this.config.width/2).attr("y",this.config.xAxisLabelBumpY).attr("text-anchor","middle").text(this.config.xLabel)};this.setUpYAxis=function(){this.yAxisFn=d3.svg.axis().scale(this.yScale).ticks(this.config.yNumTicks).orient("left");this.yAxis.call(this.yAxisFn);var i=this.yAxis.selectAll("text").filter(function(m,l){return l!==0});this.yLongestLabel=d3.max(i[0].map(function(m,l){return(d3.select(m).text()).length}))||0;var j=d+(this.yLongestLabel*h)+e+g;this.config.yAxisLabelBumpX=-(j-g);if(this.config.marginLeft<j){var k=(j)-this.config.marginLeft;k=(k<0)?(0):(k);this.adjustChartDimensions(0,0,0,k)}this.yAxisLabel.attr("x",this.config.yAxisLabelBumpX).attr("y",this.config.height/2).attr("text-anchor","middle").attr("transform",this.rotateStr(-90,this.config.yAxisLabelBumpX,this.config.height/2)).text(this.config.yLabel)};this.renderGrid=function(){this.vGridLines=this.content.selectAll("line.v-grid-line").data(this.xScale.ticks(this.xAxisFn.ticks()[0]));this.vGridLines.enter().append("svg:line").classed("grid-line v-grid-line",true);this.vGridLines.attr("x1",this.xScale).attr("y1",0).attr("x2",this.xScale).attr("y2",this.config.height);this.vGridLines.exit().remove();this.hGridLines=this.content.selectAll("line.h-grid-line").data(this.yScale.ticks(this.yAxisFn.ticks()[0]));this.hGridLines.enter().append("svg:line").classed("grid-line h-grid-line",true);this.hGridLines.attr("x1",0).attr("y1",this.yScale).attr("x2",this.config.width).attr("y2",this.yScale);this.hGridLines.exit().remove()};this.glyphEnterState=function(i){};this.glyphFinalState=function(i){};this.glyphExitState=function(i){};this.renderDatapoints=function(i,l,j){this.log(this+".renderDatapoints",arguments);var k=0;this.datapoints=this.addDatapoints(i,l,j,".glyph");this.datapoints.exit().each(function(){k+=1}).transition().duration(this.config.animDuration).attr("cy",this.config.height).attr("r",0).remove();this.log(k," glyphs removed")};this.addDatapoints=function(m,k,i,l){this.log(this+".addDatapoints",arguments);var p=this,o=0,q=function(s,r){return p.xScale(m[r])},j=function(s,r){return p.yScale(k[r])};var n=this.content.selectAll(l);this.log("existing datapoints:",n);n=n.data(m);o=0;n.enter().append("svg:circle").each(function(){o+=1}).classed("glyph",true).attr("cx",q).attr("cy",j).attr("r",0);this.log(o," new glyphs created");o=0;n.transition().duration(this.config.animDuration).each(function(){o+=1}).attr("cx",q).attr("cy",j).attr("r",p.config.datapointSize);this.log(o," existing glyphs transitioned");if(i){n.attr("data",function(s,r){return(i[r])})}n.attr("title",function(s,r){return((i)?(i[r]+": "):(""))+m[r]+", "+k[r]});n.on("mouseover",function(t,r){var s=d3.select(this);s.style("fill","red").style("fill-opacity",1);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",s.attr("cx")).attr("y1",s.attr("cy")).attr("x2",0).attr("y2",s.attr("cy")).classed("hoverline",true);p.content.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",s.attr("cx")).attr("y1",s.attr("cy")).attr("x2",s.attr("cx")).attr("y2",p.config.height).classed("hoverline",true)}).on("mouseout",function(){d3.select(this).style("fill","black").style("fill-opacity",0.2);d3.selectAll(".hoverline").remove()});return n};this.render=function(k,l){this.log(this+".render",arguments);var i=k[0],m=k[1],j=(k.length>2)?(k[2]):(undefined);i=this.preprocessData(i);m=this.preprocessData(m);this.log("xCol len",i.length,"yCol len",m.length);this.setUpDomains(i,m,l);this.setUpScales();this.adjustChartDimensions();this.setUpXAxis();this.setUpYAxis();this.renderGrid();this.renderDatapoints(i,m,j)}}var b=BaseView.extend(LoggableMixin).extend({className:"scatterplot-settings-form",dataLoadDelay:500,dataLoadSize:3001,loadingIndicatorImage:"loading_large_white_bg.gif",initialize:function(c){this.log(this+".initialize, attributes:",c);this.dataset=null;this.chartConfig=null;this.plot=null;this.loader=null;this.$statsPanel=null;this.$chartSettingsPanel=null;this.$dataSettingsPanel=null;this.dataFetch=null;this.initializeFromAttributes(c);this.initializeChart(c);this.initializeDataLoader(c)},initializeFromAttributes:function(c){if(!c||!c.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=c.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("dataset:",this.dataset);if(!c.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=c.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("this.dataURL:",this.dataURL)},initializeChart:function(c){this.chartConfig=c.chartConfig||{};if(this.logger){this.chartConfig.debugging=true}this.log("initial chartConfig:",this.chartConfig);this.plot=new a(this.chartConfig);this.chartConfig=this.plot.config},initializeDataLoader:function(d){var c=this;this.loader=new LazyDataLoader({logger:(this.logger)?(this.logger):(null),url:null,start:d.start||0,total:d.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(f,e){return this.url+"&"+jQuery.param({start_val:f,max_vals:e})}});$(this.loader).bind("error",function(g,e,f){c.log("ERROR:",e,f);alert("ERROR fetching data:\n"+e+"\n"+f);c.hideLoadingIndicator()})},render:function(){var c=this,d={config:this.chartConfig,allColumns:[],numericColumns:[],loadingIndicatorImagePath:galaxy_paths.get("image_path")+"/"+this.loadingIndicatorImage};_.each(this.dataset.metadata_column_types,function(g,f){var e="column "+(f+1);if(c.dataset.metadata_column_names){e=c.dataset.metadata_column_names[f]}if(g==="int"||g==="float"){d.numericColumns.push({index:(f+1),name:e})}d.allColumns.push({index:(f+1),name:e})});this.$el.append(b.templates.form(d));this.$dataSettingsPanel=this.$el.find(".tab-pane#data-settings");this.$chartSettingsPanel=this._render_chartSettings();this.$statsPanel=this.$el.find(".tab-pane#chart-stats");this.$dataSettingsPanel.find("#X-select").val(this.chartConfig.xColumn);this.$dataSettingsPanel.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked",true).trigger("change");this.$dataSettingsPanel.find("#ID-select").val(this.chartConfig.idColumn)}if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderPlot()}return this},isColumnNumeric:function(c){if((c>=0)&&(c<this.dataset.metadata_column_types.length)){var d=this.dataset.metadata_column_types[c];return(d==="int"||d==="float")}return false},_render_chartSettings:function(){var c=this,d=this.$el.find(".tab-pane#chart-settings"),e={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};d.append(b.templates.chartSettings(this.chartConfig));d.find(".numeric-slider-input").each(function(){var h=$(this),g=h.find(".slider-output"),i=h.find(".slider"),j=h.attr("id");function f(){var l=$(this),k=l.slider("value");g.text(k)}i.slider(_.extend(e[j],{value:c.chartConfig[j],change:f,slide:f}))});return d},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-settings #render-button":"renderPlot","click #chart-settings #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},showLoadingIndicator:function(d,e){d=d||"";var c=this.$el.find("div#loading-indicator");messageBox=c.find(".loading-message");if(c.is(":visible")){if(d){messageBox.fadeOut("fast",function(){messageBox.text(d);messageBox.fadeIn("fast",e)})}else{e()}}else{if(d){messageBox.text(d)}c.fadeIn("fast",e)}},hideLoadingIndicator:function(c){this.$el.find("div#loading-indicator").fadeOut("fast",c)},renderPlot:function(){var c=this;c.data=null;c.meta=null;_.extend(this.chartConfig,this.getGraphSettings());this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("this.loader, url:",this.loader.url,"total:",this.loader.total);$(this.loader).bind("loaded.new",function(e,d){c.log(c+" loaded.new",d);c.postProcessDataFetchResponse(d);c.log("postprocessed data:",c.data,"meta:",c.meta);c.showLoadingIndicator("Rendering...",function(){c.$el.find("ul.nav").find('a[href="#chart-stats"]').tab("show");c.plot.render(c.data,c.meta);c.renderStats(c.data,c.meta);c.hideLoadingIndicator()})});$(this.loader).bind("complete",function(d,e){c.log("complete",e);$(c.loader).unbind()});c.showLoadingIndicator("Fetching data...",function(){c.loader.load()})},renderStats:function(){this.$statsPanel.html(b.templates.statsTable({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var c=this;newGraphSettings=this.getGraphSettings();this.log("newGraphSettings:",newGraphSettings);_.extend(this.chartConfig,newGraphSettings);this.log("this.chartConfig:",this.chartConfig);this.plot.updateConfig(this.chartConfig,false);if(c.data&&c.meta){c.showLoadingIndicator("Rendering...",function(){c.plot.render(c.data,c.meta);c.hideLoadingIndicator()})}else{this.renderPlot()}},postProcessDataFetchResponse:function(c){this.postProcessData(c.data);this.postProcessMeta(c.meta)},postProcessData:function(d){var c=this;if(c.data){_.each(d,function(f,e){c.data[e]=c.data[e].concat(f)})}else{c.data=d}},postProcessMeta:function(e){var c=this,d=this.dataset.metadata_column_types;if(c.meta){_.each(e,function(g,f){var k=c.meta[f],i=d[f];c.log(f+" postprocessing meta:",g);k.count+=(g.count)?(g.count):(0);c.log(f,"count:",k.count);if((i==="int")||(i==="float")){k.min=Math.min(g.min,k.min);k.max=Math.max(g.max,k.max);k.sum=g.sum+k.sum;k.mean=(k.count)?(k.sum/k.count):(null);var h=c.data[f].slice().sort(),j=Math.floor(h.length/2);if(h.length%2===0){k.median=((h[j]+h[(j+1)])/2)}else{k.median=h[j]}}})}else{c.meta=e;c.log("initial meta:",c.meta)}},getDataSettings:function(){var d=this.getColumnSelections(),c=[];this.log("columnSelections:",d);c=[d.X.colIndex,d.Y.colIndex];if(this.$dataSettingsPanel.find("#include-id-checkbox").attr("checked")){c.push(d.ID.colIndex)}var e={data_type:"raw_data",columns:"["+c+"]"};this.log("params:",e);return e},getColumnSelections:function(){var c={};this.$dataSettingsPanel.find("div.column-select select").each(function(){var d=$(this),e=d.val();c[d.attr("name")]={colIndex:e,colName:d.children('[value="'+e+'"]').text()}});return c},getGraphSettings:function(){var e={},f=this.getColumnSelections();e.datapointSize=this.$chartSettingsPanel.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");e.width=this.$chartSettingsPanel.find("#width.numeric-slider-input").find(".slider").slider("value");e.height=this.$chartSettingsPanel.find("#height.numeric-slider-input").find(".slider").slider("value");var d=this.$chartSettingsPanel.find("input#X-axis-label").val(),c=this.$chartSettingsPanel.find("input#Y-axis-label").val();e.xLabel=(d==="X")?(f.X.colName):(d);e.yLabel=(c==="Y")?(f.Y.colName):(c);e.animDuration=10;if(this.$chartSettingsPanel.find("#animDuration.checkbox-input").is(":checked")){e.animDuration=500}this.log("graphSettings:",e);return e},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});b.templates={form:Handlebars.templates["template-visualization-scatterplotControlForm"],statsTable:Handlebars.templates["template-visualization-statsTable"],chartSettings:Handlebars.templates["template-visualization-chartSettings"]};return{LazyDataLoader:LazyDataLoader,TwoVarScatterplot:a,ScatterplotControlForm:b}}); \ 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: dannon: Adjust sqlalchemy import ordering, fixes functional test running.
by Bitbucket 20 Nov '12

20 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/67b9614dcab4/ changeset: 67b9614dcab4 user: dannon date: 2012-11-20 19:05:32 summary: Adjust sqlalchemy import ordering, fixes functional test running. affected #: 1 file diff -r e856e0b90cd21338e27c385e9615612715bc7632 -r 67b9614dcab440027292c5dc387ef2eb1a763c19 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -9,8 +9,6 @@ pkg_resources.require("simplejson") pkg_resources.require("pexpect") import simplejson, os, errno, codecs, operator, socket, pexpect, logging, time -from sqlalchemy.orm import object_session -from sqlalchemy.sql.expression import func import galaxy.datatypes import galaxy.datatypes.registry from galaxy.datatypes.metadata import MetadataCollection @@ -21,6 +19,8 @@ from galaxy.web.form_builder import (AddressField, CheckboxField, PasswordField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField) from galaxy.model.item_attrs import UsesAnnotations, APIItem +from sqlalchemy.orm import object_session +from sqlalchemy.sql.expression import func log = logging.getLogger( __name__ ) 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: richard_burhans: updates to Phenotype Association tools from Belinda
by Bitbucket 20 Nov '12

20 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e856e0b90cd2/ changeset: e856e0b90cd2 user: richard_burhans date: 2012-11-20 17:42:13 summary: updates to Phenotype Association tools from Belinda affected #: 16 files Diff too large to display. 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: Extend the tool shed functional test framework.
by Bitbucket 20 Nov '12

20 Nov '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d69b780edd18/ changeset: d69b780edd18 user: inithello date: 2012-11-20 15:17:41 summary: Extend the tool shed functional test framework. affected #: 3 files diff -r 0741ac889c4b85286a9baadcf6110f3e052a79f0 -r d69b780edd1816171c2751e2ce4d987f7254019e test/tool_shed/base/test_db_util.py --- a/test/tool_shed/base/test_db_util.py +++ b/test/tool_shed/base/test_db_util.py @@ -2,6 +2,7 @@ from galaxy.model.orm import * from galaxy.webapps.community.model.mapping import context as sa_session from base.twilltestcase import * +from sqlalchemy import desc import sys def delete_obj( obj ): @@ -31,9 +32,20 @@ return sa_session.query( model.User ) \ .filter( model.User.table.c.email==email ) \ .first() +def get_user_by_name( username ): + return sa_session.query( model.User ) \ + .filter( model.User.table.c.username==username ) \ + .first() def mark_obj_deleted( obj ): obj.deleted = True sa_session.add( obj ) sa_session.flush() def refresh( obj ): sa_session.refresh( obj ) +def get_repository_by_name( name, owner_username ): + owner = get_user_by_name( owner_username ) + repository = sa_session.query( model.Repository ) \ + .filter( model.Repository.table.c.name==name ) \ + .filter( model.Repository.table.c.user_id==owner.id ) \ + .first() + return repository diff -r 0741ac889c4b85286a9baadcf6110f3e052a79f0 -r d69b780edd1816171c2751e2ce4d987f7254019e test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1,4 +1,5 @@ from base.twilltestcase import * +from tool_shed.base.test_db_util import * class ShedTwillTestCase( TwillTestCase ): def setUp( self ): @@ -18,3 +19,123 @@ except: pass self.home() + def browse_repository( self, repository, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository/browse_repository?id=%s' % self.security.encode_id( repository.id ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def check_for_strings( self, strings_displayed=[], strings_not_displayed=[] ): + if strings_displayed: + for string in strings_displayed: + self.check_page_for_string( string ) + if strings_not_displayed: + for string in strings_not_displayed: + self.check_string_not_in_page( string ) + def check_for_valid_tools( self, repository ): + self.manage_repository( repository ) + self.check_page_for_string( '<b>Valid tools</b><i> - click the name to preview the tool' ) + def check_repository_changelog( self, repository, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository/view_changelog?id=%s' % self.security.encode_id( repository.id ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def create_category( self, category_name, category_description ): + self.visit_url( '/admin/manage_categories?operation=create' ) + tc.fv( "1", "name", category_name ) + tc.fv( "1", "description", category_description ) + tc.submit( "create_category_button" ) + def create_repository( self, repository_name, repository_description, repository_long_description=None, categories=[], strings_displayed=[], strings_not_displayed=[] ): + self.visit_url( '/repository/create_repository' ) + tc.fv( "1", "name", repository_name ) + tc.fv( "1", "description", repository_description ) + if repository_long_description is not None: + tc.fv( "1", "long_description", repository_long_description ) + for category in categories: + tc.fv( "1", "category_id", "+%s" % category ) + tc.submit( "create_repository_button" ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_repository_clone_page( self, owner_name, repository_name, strings_displayed=[], strings_not_displayed=[] ): + url = '/repos/%s/%s' % ( owner_name, repository_name ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def edit_repository_categories( self, repository, categories_to_add=[], categories_to_remove=[], restore_original=True ): + url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) + self.visit_url( url ) + strings_displayed = [] + strings_not_displayed = [] + for category in categories_to_add: + tc.fv( "2", "category_id", '+%s' % category) + strings_displayed.append( "selected>%s</option>" % category ) + for category in categories_to_remove: + tc.fv( "2", "category_id", '-%s' % category) + strings_not_displayed.append( "selected>%s</option>" % category ) + tc.submit( "manage_categories_button" ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + if restore_original: + strings_displayed = [] + strings_not_displayed = [] + for category in categories_to_remove: + tc.fv( "2", "category_id", '+%s' % category) + strings_displayed.append( "selected>%s</option>" % category ) + for category in categories_to_add: + tc.fv( "2", "category_id", '-%s' % category) + strings_not_displayed.append( "selected>%s</option>" % category ) + tc.submit( "manage_categories_button" ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def edit_repository_information( self, repository, **kwargs ): + url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) + self.visit_url( url ) + original_information = dict( repo_name=repository.name, description=repository.description, long_description=repository.long_description ) + strings_displayed = [] + strings_not_displayed = [] + for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: + if input_elem_name in kwargs: + tc.fv( "1", input_elem_name, kwargs[ input_elem_name ] ) + strings_displayed.append( self.escape_html( kwargs[ input_elem_name ] ) ) + tc.submit( "edit_repository_button" ) + self.check_for_strings( strings_displayed ) + strings_displayed = [] + for input_elem_name in [ 'repo_name', 'description', 'long_description' ]: + tc.fv( "1", input_elem_name, original_information[ input_elem_name ] ) + strings_displayed.append( self.escape_html( original_information[ input_elem_name ] ) ) + tc.submit( "edit_repository_button" ) + self.check_for_strings( strings_displayed ) + def escape_html( self, string ): + html_entities = [ ('&', 'X' ), ( "'", ''' ), ( '"', '"' ) ] + for character, replacement in html_entities: + string = string.replace( character, replacement ) + return string + def get_latest_repository_metadata_for_repository( self, repository ): + return repository.metadata_revisions[ 0 ] + def get_readme( self, repository, strings_displayed=[], strings_not_displayed=[] ): + repository_metadata = self.get_latest_repository_metadata_for_repository( repository ) + changeset_revision = repository_metadata.changeset_revision + repository_id = self.security.encode_id( repository.id ) + self.visit_url( '/repository/view_readme?changeset_revision=%s&id=%s' % ( changeset_revision, repository_id ) ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def grant_write_access( self, repository, usernames=[], strings_displayed=[], strings_not_displayed=[] ): + self.manage_repository( repository ) + tc.fv( "3", "allow_push", '-Select one' ) + for username in usernames: + tc.fv( "3", "allow_push", '+%s' % username ) + tc.submit( 'user_access_button' ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def manage_repository( self, repository, strings_displayed=[], strings_not_displayed=[] ): + url = '/repository/manage_repository?id=%s' % self.security.encode_id( repository.id ) + self.visit_url( url ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def set_repository_malicious( self, repository, strings_displayed=[], strings_not_displayed=[] ): + self.manage_repository( repository ) + tc.fv( "malicious", "malicious", True ) + tc.submit( "malicious_button" ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def unset_repository_malicious( self, repository, strings_displayed=[], strings_not_displayed=[] ): + self.manage_repository( repository ) + tc.fv( "malicious", "malicious", False ) + tc.submit( "malicious_button" ) + self.check_for_strings( strings_displayed, strings_not_displayed ) + def upload( self, repository, filename, strings_displayed=[], strings_not_displayed=[], **kwargs ): + self.visit_url( '/upload/upload?repository_id=%s' % self.security.encode_id( repository.id ) ) + for key in kwargs: + tc.fv( "1", key, kwargs[ key ] ) + tc.formfile( "1", "file_data", filename ) + tc.submit( "upload_button" ) + self.check_for_strings( strings_displayed, strings_not_displayed ) diff -r 0741ac889c4b85286a9baadcf6110f3e052a79f0 -r d69b780edd1816171c2751e2ce4d987f7254019e test/tool_shed/functional/test_0000_create_repository.py --- a/test/tool_shed/functional/test_0000_create_repository.py +++ b/test/tool_shed/functional/test_0000_create_repository.py @@ -11,34 +11,77 @@ admin_email = 'test(a)bx.psu.edu' admin_username = 'admin-user' +regular_user = None +regular_user_private_role = None +regular_email = 'test-1(a)bx.psu.edu' +regular_username = 'user1' + +repository_name = 'filter' +repository_description = "Galaxy's filter tool" +repository_long_description = "Long description of Galaxy's filter tool" +files_path = os.path.abspath( os.path.join( "test", "tool_shed", "test_data" ) ) +filter_filename = os.path.join( files_path, "filtering_1.1.0.tar" ) + class TestCreateRepository( ShedTwillTestCase ): def test_0000_initiate_users( self ): """Create necessary users and login as an admin user.""" + self.login( email=regular_email, username=regular_username ) + regular_user = get_user( regular_email ) + assert regular_user is not None, 'Problem retrieving user with email %s from the database' % regular_email + regular_user_private_role = get_private_role( regular_user ) self.logout() self.login( email=admin_email, username=admin_username ) admin_user = get_user( admin_email ) assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email admin_user_private_role = get_private_role( admin_user ) - def test_0005_create_category( self ): + def test_0005_create_categories( self ): """Create a category""" - self.visit_url( '/admin/manage_categories?operation=create' ) - try: - tc.fv( "1", "name", "Text Manipulation" ) - tc.fv( "1", "description", "Tools for manipulating text" ) - tc.submit( "create_category_button" ) - except Exception, e: - errmsg = "Problem creating a category: %s" % str( e ) - raise AssertionError( e ) - def test_0010_create_filter_repository( self ): + self.create_category( 'Text Manipulation', 'Tools for manipulating text' ) + self.create_category( 'Text Analysis', 'Tools for analyzing text' ) + def test_0010_create_repository( self ): """Create a repository""" - self.visit_url( '/repository/create_repository' ) - try: - tc.fv( "1", "name", "filter" ) - tc.fv( "1", "description", "Galaxy's filter tool" ) - tc.fv( "1", "long_description", "Long description of Galaxy's filter tool" ) - tc.fv( "1", "category_id", "Text Manipulation" ) - tc.submit( "create_repository_button" ) - except Exception, e: - errmsg = "Problem creating a repository: %s" % str( e ) - raise AssertionError( e ) + strings_displayed = [ '<div class="toolFormTitle">Repository %s</div>' % "'%s'" % repository_name, \ + 'Repository %s has been created' % "'%s'" % repository_name ] + self.create_repository( repository_name, repository_description, \ + repository_long_description=repository_long_description, \ + categories=[ 'Text Manipulation' ], \ + strings_displayed=strings_displayed ) + def test_0015_edit_repository( self ): + """Edit the repository name, description, and long description""" + repository = get_repository_by_name( repository_name, admin_username ) + new_name = "renamed_filter" + new_description = "Edited filter tool" + new_long_description = "Edited long description" + self.edit_repository_information( repository, repo_name=new_name, description=new_description, long_description=new_long_description ) + def test_0020_change_repository_category( self ): + """Change the category of a repository""" + repository = get_repository_by_name( repository_name, admin_username ) + self.edit_repository_categories( repository, categories_to_add=[ "Text Analysis" ], categories_to_remove=[ "Text Manipulation" ] ) +# def test_0025_grant_write_access( self ): +# '''Grant write access to another user''' +# repository = get_repository_by_name( repository_name, admin_username ) +# self.grant_write_access( repository, usernames=[ regular_username ] ) + def test_0030_upload_tarball( self ): + """Upload filtering_1.1.0.tar to the repository""" + repository = get_repository_by_name( repository_name, admin_username ) + self.upload( repository, filter_filename, \ + strings_displayed=[ "The file '%s' has been successfully uploaded to the repository." % filter_filename ], \ + commit_message="Uploaded filtering 1.1.0" ) + self.check_for_valid_tools( repository ) + latest_changeset_revision = self.get_latest_repository_metadata_for_repository( repository ) + self.check_repository_changelog( repository, strings_displayed=[ 'Repository metadata is associated with this change set.' ] ) + self.set_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as malicious.' ] ) + self.unset_repository_malicious( repository, strings_displayed=[ 'The repository tip has been defined as <b>not</b> malicious.' ] ) +# self.check_tool_metadata( repository, latest_changeset_revision, strings_displayed=[ 'Filter1' ] ) + def test_0035_repository_browse_page( self ): + '''Visit the repository browse page''' + repository = get_repository_by_name( repository_name, admin_username ) + self.browse_repository( repository, strings_displayed=[ 'Browse %s revision' % repository.name, '(repository tip)' ] ) + def test_0040_visit_clone_url_via_hgweb( self ): + '''Visit the repository clone URL via hgweb''' + repository = get_repository_by_name( repository_name, admin_username ) + latest_changeset_revision = self.get_latest_repository_metadata_for_repository( repository ) + self.display_repository_clone_page( admin_username, \ + repository_name, \ + strings_displayed=[ 'Uploaded filtering 1.1.0', latest_changeset_revision.changeset_revision ] ) 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