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commit/galaxy-central: greg: Fixes for handling repository dependencies in the tool shed.
by Bitbucket 06 Dec '12

06 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/75e427a748d0/ changeset: 75e427a748d0 user: greg date: 2012-12-06 23:00:54 summary: Fixes for handling repository dependencies in the tool shed. affected #: 2 files diff -r 7b791a48be76604324f23445293d55948f789dde -r 75e427a748d0b3e89ccdf246f22499c2f44d9e2a lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1200,7 +1200,6 @@ if 'description' not in all_repository_dependencies: description = repository_dependencies_dict.get( 'description', None ) all_repository_dependencies[ 'description' ] = description - # The next key of interest in repository_dependencies_dict is 'repository_dependencies', which is a list of tuples. repository_dependencies_tups = repository_dependencies_dict[ 'repository_dependencies' ] for repository_dependency in repository_dependencies_tups: @@ -1231,6 +1230,7 @@ else: # Insert this repository_dependency. all_repository_dependencies[ repository_dependencies_root_key ] = [ repository_dependency ] + handled.append( repository_dependency ) if tool_shed_is_this_tool_shed( tool_shed ): # The repository is in the current tool shed. required_repository = get_repository_by_name_and_owner( trans, name, owner ) diff -r 7b791a48be76604324f23445293d55948f789dde -r 75e427a748d0b3e89ccdf246f22499c2f44d9e2a lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -36,7 +36,14 @@ listified_repository_dependency = repository_dependency.listify for contained_repository_dependency in self.repository_dependencies: if contained_repository_dependency.listify == listified_repository_dependency: - self.repository_dependencies.remove( contained_repository_dependency ) + self.repository_dependencies.remove( contained_repository_dependency ) + def to_repository_dependency( self, repository_dependency_id ): + toolshed, name, owner, changeset_revision = self.key.split( STRSEP ) + return RepositoryDependency( id=repository_dependency_id, + toolshed=toolshed, + repository_name=name, + repository_owner=owner, + changeset_revision=changeset_revision ) class Datatype( object ): """Datatype object""" @@ -199,36 +206,45 @@ # Create the Repository dependencies folder and add it to the root folder. repository_dependencies_folder_key = repository_dependencies[ 'root_key' ] repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label, parent=repository_dependencies_root_folder ) - # The received repository_dependencies is a dictionary with a single 'description' key, and one or more repository_dependency keys. + del repository_dependencies[ 'root_key' ] + # The received repository_dependencies is a dictionary with keys: 'root_key', 'description', and one or more repository_dependency keys. # We want the description value associated with the repository_dependencies_folder. repository_dependencies_folder.description = repository_dependencies.get( 'description', None ) repository_dependencies_root_folder.folders.append( repository_dependencies_folder ) + del repository_dependencies[ 'description' ] + # The remaining keys in repository_dependencies should all be folders. + folder_keys = repository_dependencies.keys() + # If repository_dependencies_folder_key is an entry in repository_dependencies, process it first. + if repository_dependencies_folder_key in repository_dependencies: + val = repository_dependencies[ repository_dependencies_folder_key ] + repository_dependencies_folder, folder_id, repository_dependency_id = handle_repository_dependencies_entry( repository_dependencies_root_folder, + repository_dependencies_folder, + repository_dependencies_folder_key, + folder_keys, + folder_id, + repository_dependency_id, + repository_name, + repository_owner, + changeset_revision, + repository_dependencies_folder_key, + val ) + del repository_dependencies[ repository_dependencies_folder_key ] for key, val in repository_dependencies.items(): - if key in [ 'root_key', 'description' ]: - continue - # Only create a new folder object if necessary. - folder = get_folder( repository_dependencies_root_folder, key ) - if not folder: - # Create a new folder. - folder_id += 1 - label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ) - folder = Folder( id=folder_id, key=key, label=label, parent=repository_dependencies_folder ) - for repository_dependency_tup in val: - toolshed, name, owner, changeset_revision = repository_dependency_tup - # Create a new repository_dependency. - repository_dependency_id += 1 - repository_dependency = RepositoryDependency( id=repository_dependency_id, - toolshed=toolshed, - repository_name=name, - repository_owner=owner, - changeset_revision=changeset_revision ) - # Insert the repository_dependency into the folder. - folder.repository_dependencies.append( repository_dependency ) - if not get_folder( repository_dependencies_folder, key ): - # Insert the folder into the list. - repository_dependencies_folder.folders.append( folder ) + repository_dependencies_folder, folder_id, repository_dependency_id = handle_repository_dependencies_entry( repository_dependencies_root_folder, + repository_dependencies_folder, + repository_dependencies_folder_key, + folder_keys, + folder_id, + repository_dependency_id, + repository_name, + repository_owner, + changeset_revision, + key, + val ) + # Cast empty folders to be repository dependencies. + repository_dependencies_folder, repository_dependency_id = cast_empty_repository_dependency_folders( repository_dependencies_folder, + repository_dependency_id ) # Remove repository_dependencies that are also folders, and coerce empty folders into repository dependencies. - prune_repository_dependencies( repository_dependencies_folder, repository_dependencies_folder ) else: repository_dependencies_root_folder = None return folder_id, repository_dependencies_root_folder @@ -360,13 +376,23 @@ else: workflows_root_folder = None return folder_id, workflows_root_folder +def cast_empty_repository_dependency_folders( folder, repository_dependency_id ): + if not folder.folders and not folder.repository_dependencies: + repository_dependency_id += 1 + repository_dependency = folder.to_repository_dependency( repository_dependency_id ) + if not folder.parent.contains_repository_dependency( repository_dependency ): + folder.parent.repository_dependencies.append( repository_dependency ) + folder.parent.folders.remove( folder ) + for sub_folder in folder.folders: + return cast_empty_repository_dependency_folders( sub_folder, repository_dependency_id ) + return folder, repository_dependency_id def generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ): """Return a repository dependency label based on the repository dependency key.""" if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): label = 'Repository dependencies' else: - toolshed_base_url, name, owner, revision = get_components_from_key( key ) - label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( name, revision, owner ) + #toolshed_base_url, name, owner, revision = get_components_from_key( key ) + label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( repository_name, changeset_revision, repository_owner ) return label def generate_repository_dependencies_key_for_repository( toolshed_base_url, repository_name, repository_owner, changeset_revision ): # FIXME: assumes tool shed is current tool shed since repository dependencies across tool sheds is not yet supported. @@ -391,25 +417,61 @@ repository_owner = items[ 2 ] changeset_revision = items[ 3 ] return toolshed_base_url, repository_name, repository_owner, changeset_revision -def is_folder( folder_keys, toolshed_base_url, repository_name, repository_owner, changeset_revision ): - key = '%s%s%s%s%s%s%s' % ( toolshed_base_url, STRSEP, repository_name, STRSEP, repository_owner, STRSEP, changeset_revision ) +def handle_repository_dependencies_entry( repository_dependencies_root_folder, repository_dependencies_folder, repository_dependencies_folder_key, + folder_keys, folder_id, repository_dependency_id, repository_name, repository_owner, changeset_revision, + key, val ): + # Only create a new folder object if necessary. + folder = get_folder( repository_dependencies_root_folder, key ) + if not folder: + folder_id += 1 + label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ) + folder = Folder( id=folder_id, key=key, label=label, parent=repository_dependencies_folder ) + for repository_dependency_tup in val: + toolshed, name, owner, changeset_revision = repository_dependency_tup + if is_root_repository( repository_dependencies_folder_key, toolshed, name, owner ): + # Do not include repository dependencies that point to a revision within the same repository. + continue + if is_or_should_be_folder( folder_keys, toolshed, name, owner, changeset_revision ): + check_folder_key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision ) + if get_folder( repository_dependencies_root_folder, check_folder_key ): + continue + else: + # Create a new folder, which may be populated later. + folder_id += 1 + label = generate_repository_dependencies_folder_label_from_key( name, owner, changeset_revision, key ) + sub_folder = Folder( id=folder_id, key=check_folder_key, label=label, parent=repository_dependencies_folder ) + folder.folders.append( sub_folder ) + else: + repository_dependency_id += 1 + repository_dependency = RepositoryDependency( id=repository_dependency_id, + toolshed=toolshed, + repository_name=name, + repository_owner=owner, + changeset_revision=changeset_revision ) + # Insert the repository_dependency into the folder. + folder.repository_dependencies.append( repository_dependency ) + if not get_folder( repository_dependencies_folder, folder.key ): + if folder.folders: + # Insert the folder into the list. + repository_dependencies_folder.folders.append( folder ) + return repository_dependencies_folder, folder_id, repository_dependency_id +def is_or_should_be_folder( folder_keys, toolshed, repository_name, repository_owner, changeset_revision ): + key = '%s%s%s%s%s%s%s' % ( toolshed, STRSEP, repository_name, STRSEP, repository_owner, STRSEP, changeset_revision ) return key in folder_keys +def is_root_repository( repository_dependencies_folder_key, toolshed, repository_name, repository_owner ): + # Return True if a repository dependency points to a revision within it's own repository. + repository_dependencies_folder_tup = repository_dependencies_folder_key.split( STRSEP ) + rdf_toolshed, rdf_repository_name, rdf_repository_owner, rdf_changeset_revision = repository_dependencies_folder_tup + return rdf_toolshed == toolshed and rdf_repository_name == repository_name and rdf_repository_owner == repository_owner def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key ) return repository_name == key_name and repository_owner == key_owner and changeset_revision == key_changeset_revision -def prune_folder( folder, repository_dependency, key ): - if get_folder( folder, key ): - folder.remove_repository_dependency( repository_dependency ) +def print_folders( pad, folder ): + # For debugging... + pad_str = '' + for i in range( 1, pad ): + pad_str += ' ' + print '%s%s' % ( pad_str, folder.key ) for sub_folder in folder.folders: - prune_folder( sub_folder, repository_dependency, key ) -def prune_repository_dependencies( folder, root_folder ): - """Remove repository_dependencies that are also folders, and coerce empty folders into repository dependencies.""" - remove_repository_dependencies( folder, root_folder ) - for sub_folder in folder.folders: - prune_repository_dependencies( sub_folder, root_folder ) -def remove_repository_dependencies( folder, root_folder ): - for repository_dependency in folder.repository_dependencies: - toolshed, name, owner, changeset_revision = repository_dependency.listify - key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision ) - prune_folder( root_folder, repository_dependency, key ) + print_folders( pad+5, sub_folder ) \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: history panel: fix download popup for uploaded files with meta files (bam) by moving url rendering from initialize to render; pack scripts
by Bitbucket 06 Dec '12

06 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7b791a48be76/ changeset: 7b791a48be76 user: carlfeberhard date: 2012-12-06 22:33:18 summary: history panel: fix download popup for uploaded files with meta files (bam) by moving url rendering from initialize to render; pack scripts affected #: 5 files diff -r 78a3508c456296bd7bd578f5c8dd121d7206fef8 -r 7b791a48be76604324f23445293d55948f789dde static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -35,12 +35,9 @@ this._render_showParamsButton ]; - // render urlTemplates (gen. provided by GalaxyPaths) to urls - //TODO:?? render urls here or in render()? + // cache urlTemplates (gen. provided by GalaxyPaths) to urls if( !attributes.urlTemplates ){ throw( 'HDAView needs urlTemplates on initialize' ); } - /** web controller urls for functions relating to this hda. These - * are rendered from urlTemplates using the model data. */ - this.urls = this._renderUrls( attributes.urlTemplates, this.model.toJSON() ); + this.urlTemplates = attributes.urlTemplates; /** is the body of this hda view expanded/not. */ this.expanded = attributes.expanded || false; @@ -52,6 +49,61 @@ //}, this ); }, + // ......................................................................... RENDER MAIN + /** Render this HDA, set up ui. + * @fires rendered:ready when rendered and NO running HDAs + * @fires rendered when rendered and running HDAs + * @fires rendered:initial on first render with running HDAs + * @fires rendered:initial:ready when first rendered and NO running HDAs + * @returns {Object} this HDABaseView + */ + render : function(){ + var view = this, + id = this.model.get( 'id' ), + state = this.model.get( 'state' ), + itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ), + initialRender = ( this.$el.children().size() === 0 ); + + this.$el.attr( 'id', 'historyItemContainer-' + id ); + + /** web controller urls for functions relating to this hda. + * These are rendered from urlTemplates using the model data. */ + this.urls = this._renderUrls( this.urlTemplates, this.model.toJSON() ); + + itemWrapper + .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) + .addClass( 'historyItem-' + state ); + + itemWrapper.append( this._render_warnings() ); + itemWrapper.append( this._render_titleBar() ); + this.body = $( this._render_body() ); + itemWrapper.append( this.body ); + + //TODO: move to own function: setUpBehaviours + // we can potentially skip this step and call popupmenu directly on the download button + make_popup_menus( itemWrapper ); + + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) + itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); + + // transition... + this.$el.fadeOut( 'fast', function(){ + view.$el.children().remove(); + view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ + view.log( view + ' rendered:', view.$el ); + + var renderedEventName = 'rendered'; + if( initialRender ){ + renderedEventName += ':initial'; + } else if( view.model.inReadyState() ){ + renderedEventName += ':ready'; + } + view.trigger( renderedEventName ); + }); + }); + return this; + }, + /** render the urls for this hda using the model data and the url templates from initialize. * @param {Object} urlTemplates a map (or nested map) of underscore templates (currently, anyhoo) * @param {Object} modelJson data from the model @@ -71,6 +123,7 @@ //TODO: should be a better (gen.) way to handle this case if( urlKey === 'meta_download' ){ urls[ urlKey ] = hdaView._renderMetaDownloadUrls( urlTemplateOrObj, modelJson ); + } else { try { urls[ urlKey ] = _.template( urlTemplateOrObj, modelJson ); @@ -100,57 +153,6 @@ }); }, - // ......................................................................... RENDER MAIN - /** Render this HDA, set up ui. - * @fires rendered:ready when rendered and NO running HDAs - * @fires rendered when rendered and running HDAs - * @fires rendered:initial on first render with running HDAs - * @fires rendered:initial:ready when first rendered and NO running HDAs - * @returns {Object} this HDABaseView - */ - render : function(){ - var view = this, - id = this.model.get( 'id' ), - state = this.model.get( 'state' ), - itemWrapper = $( '<div/>' ).attr( 'id', 'historyItem-' + id ), - initialRender = ( this.$el.children().size() === 0 ); - - this.$el.attr( 'id', 'historyItemContainer-' + id ); - - itemWrapper - .addClass( 'historyItemWrapper' ).addClass( 'historyItem' ) - .addClass( 'historyItem-' + state ); - - itemWrapper.append( this._render_warnings() ); - itemWrapper.append( this._render_titleBar() ); - this.body = $( this._render_body() ); - itemWrapper.append( this.body ); - - //TODO: move to own function: setUpBehaviours - // we can potentially skip this step and call popupmenu directly on the download button - make_popup_menus( itemWrapper ); - - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - itemWrapper.find( '.tooltip' ).tooltip({ placement : 'bottom' }); - - // transition... - this.$el.fadeOut( 'fast', function(){ - view.$el.children().remove(); - view.$el.append( itemWrapper ).fadeIn( 'fast', function(){ - view.log( view + ' rendered:', view.$el ); - - var renderedEventName = 'rendered'; - if( initialRender ){ - renderedEventName += ':initial'; - } else if( view.model.inReadyState() ){ - renderedEventName += ':ready'; - } - view.trigger( renderedEventName ); - }); - }); - return this; - }, - // ................................................................................ RENDER titlebar /** Render any hda warnings including: is deleted, is purged, is hidden. * (including links to further actions (undelete, etc.)) diff -r 78a3508c456296bd7bd578f5c8dd121d7206fef8 -r 7b791a48be76604324f23445293d55948f789dde static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -var HDABaseView=BaseView.extend(LoggableMixin).extend({tagName:"div",className:"historyItemContainer",initialize:function(a){this.log(this+".initialize:",a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];if(!a.urlTemplates){throw ("HDAView needs urlTemplates on initialize")}this.urls=this._renderUrls(a.urlTemplates,this.model.toJSON());this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},_renderUrls:function(d,a){var b=this,c={};_.each(d,function(e,f){if(_.isObject(e)){c[f]=b._renderUrls(e,a)}else{if(f==="meta_download"){c[f]=b._renderMetaDownloadUrls(e,a)}else{c[f]=_.template(e,a)}}});return c},_renderMetaDownloadUrls:function(b,a){return _.map(a.meta_files,function(c){return{url:_.template(b,{id:a.id,file_type:c.file_type}),file_type:c.file_type}})},render:function(){var b=this,e=this.model.get("id"),c=this.model.get("state"),a=$("<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=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());return a},_render_displayButton:function(){if((!this.model.inReadyState())||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.displayButton=null;return null}var a={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){a.enabled=false;a.title=_l("Cannot display datasets removed from disk")}else{a.title=_l("Display data in browser");a.href=this.urls.display}this.displayButton=new IconButtonView({model:new IconButton(a)});return this.displayButton.render().$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.urlTemplates=a.urlTemplates;this.expanded=a.expanded||false;this.model.bind("change",this.render,this)},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.$el.attr("id","historyItemContainer-"+e);this.urls=this._renderUrls(this.urlTemplates,this.model.toJSON());a.addClass("historyItemWrapper").addClass("historyItem").addClass("historyItem-"+c);a.append(this._render_warnings());a.append(this._render_titleBar());this.body=$(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},_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{try{c[f]=_.template(e,a)}catch(g){throw (b+"._renderUrls error: "+g+"\n rendering:"+e+"\n with "+JSON.stringify(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_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 "'+this.model.get("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"))})}},remove:function(){},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 78a3508c456296bd7bd578f5c8dd121d7206fef8 -r 7b791a48be76604324f23445293d55948f789dde static/scripts/packed/mvc/dataset/hda-model.js --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1,1 +1,1 @@ -var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"",state:"",data_type:null,file_size:0,meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:false},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.NEW)||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return}var b=this;_.each(a,function(e,c){var d=b.get(e);d.fetch()})},toString:function(){return("HDACollection("+this.ids().join(",")+")")}}); \ No newline at end of file +var HistoryDatasetAssociation=BaseModel.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"ok",data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",deleted:false,purged:false,visible:false,accessible:true},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("history_id")+"/contents/"+this.get("id")},initialize:function(){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",HistoryDatasetAssociation.STATES.NOT_VIEWABLE)}this.on("change:state",function(b,a){this.log(this+" has changed state:",b,a);if(this.inReadyState()){this.trigger("state:ready",this.get("id"),a,this.previous("state"),b)}})},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(b,c){var a=true;if((!b)&&(this.get("deleted")||this.get("purged"))){a=false}if((!c)&&(!this.get("visible"))){a=false}return a},inReadyState:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.NEW)||(a===HistoryDatasetAssociation.STATES.OK)||(a===HistoryDatasetAssociation.STATES.EMPTY)||(a===HistoryDatasetAssociation.STATES.FAILED_METADATA)||(a===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(a===HistoryDatasetAssociation.STATES.DISCARDED)||(a===HistoryDatasetAssociation.STATES.ERROR))},hasData:function(){return(this.get("file_size")>0)},toString:function(){var a=this.get("id")||"";if(this.get("name")){a+=':"'+this.get("name")+'"'}return"HistoryDatasetAssociation("+a+")"}});HistoryDatasetAssociation.STATES={UPLOAD:"upload",QUEUED:"queued",PAUSED:"paused",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};var HDACollection=Backbone.Collection.extend(LoggableMixin).extend({model:HistoryDatasetAssociation,initialize:function(){},ids:function(){return this.map(function(a){return a.id})},hidToCollectionIndex:function(a){if(!a){return this.models.length}var d=this.models.length-1;for(var b=d;b>=0;b--){var c=this.at(b).get("hid");if(c==a){return b}if(c<a){return b+1}}return null},getVisible:function(a,b){return this.filter(function(c){return c.isVisible(a,b)})},getStateLists:function(){var a={};_.each(_.values(HistoryDatasetAssociation.STATES),function(b){a[b]=[]});this.each(function(b){a[b.get("state")].push(b.get("id"))});return a},running:function(){var a=[];this.each(function(b){if(!b.inReadyState()){a.push(b.get("id"))}});return a},update:function(a){this.log(this+"update:",a);if(!(a&&a.length)){return[]}var c=this,b=null;_.each(a,function(f,d){var e=c.get(f);if(e){e.fetch();b.push(e)}});return b},toString:function(){return("HDACollection()")}}); \ No newline at end of file diff -r 78a3508c456296bd7bd578f5c8dd121d7206fef8 -r 7b791a48be76604324f23445293d55948f789dde static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.hdas.update(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},4000)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e)}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=BaseModel.extend(LoggableMixin).extend({defaults:{id:"",name:"",state:"",diskSize:0,deleted:false,annotation:null,message:null},urlRoot:"api/histories/",url:function(){return"api/histories/"+this.get("id")},initialize:function(a,b){this.log(this+".initialize:",a,b);this.hdas=new HDACollection();if(b&&b.length){this.hdas.reset(b);this.checkForUpdates()}},loadFromApi:function(a,c){var b=this;b.attributes.id=a;jQuery.when(jQuery.ajax("api/users/current"),b.fetch()).then(function(e,d){b.attributes.user=e[0];b.trigger("loaded:user",e[0]);b.trigger("loaded",d[0])}).then(function(){jQuery.ajax(b.url()+"/contents?"+jQuery.param({ids:b.hdaIdsFromStateIds().join(",")})).success(function(d){b.hdas.reset(d);b.checkForUpdates();b.trigger("loaded:hdas",d);if(c){callback(b)}})})},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},checkForUpdates:function(a){if(this.hdas.running().length){this.stateUpdater()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=[];_.each(_.keys(d.state_ids),function(g){var f=_.difference(d.state_ids[g],b[g]);e=e.concat(f)});if(e.length){c.updateHdas(e)}if((c.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(c.get("state")===HistoryDatasetAssociation.STATES.QUEUED)){setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.trigger("ready")}}).error(function(f,d,e){if(!((f.readyState===0)&&(f.status===0))){alert(_l("Error getting history updates from the server.")+"\n"+e)}})},updateHdas:function(b){var a=this;jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:b.join(",")}),error:function(f,c,d){var e="ERROR updating hdas from api history contents:";a.log(e,b,f,c,d);alert(e+b.join(","))},success:function(d,c,f){a.log(a+".updateHdas, success:",d,c,f);var e=[];_.each(d,function(h,i){var g=a.hdas.get(h.id);if(g){a.log("found existing model in list for id "+h.id+", updating...:");g.set(h)}else{a.log("NO existing model for id "+h.id+", creating...:");modelsToAdd.push(h)}});if(e.length){a.addHdas(e)}}})},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e})})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r 78a3508c456296bd7bd578f5c8dd121d7206fef8 -r 7b791a48be76604324f23445293d55948f789dde 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-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 +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.model.hdas.bind("change:state",function(c,d,b){if((c.inReadyState())&&(!c.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHda(c)}},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){this.render()},addAll:function(){this.render()},removeHda:function(a,c){var b=this.hdaViews[a.get("id")];b.$el.fadeOut("fast",function(){b.$el.remove();if(c){c()}});this.model.hdas.remove(a)},render:function(){var b=this,d=b.toString()+".set-up",c=$("<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 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 06 Dec '12

06 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/801e7cf8227f/ changeset: 801e7cf8227f user: dan date: 2012-12-06 22:26:02 summary: Fix for text area formbuilder when None is provided for size. affected #: 1 file diff -r 449f0ed92b4621093d2e1b38dee5894f2a9b959e -r 801e7cf8227fd2b9294a6140d0580b3c78f705fe lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -67,8 +67,10 @@ >>> print TextArea( "bins", size="4x5", value="default" ).get_html() <textarea name="bins" rows="4" cols="5">default</textarea> """ - def __init__( self, name, size="5x25", value=None ): + _DEFAULT_SIZE = "5x25" + def __init__( self, name, size=None, value=None ): self.name = name + size = size or self._DEFAULT_SIZE self.size = size.split("x") self.rows = int(self.size[0]) self.cols = int(self.size[-1]) https://bitbucket.org/galaxy/galaxy-central/changeset/78a3508c4562/ changeset: 78a3508c4562 user: dan date: 2012-12-06 22:26:02 summary: Fix for error reporting link due to client-side history change (id is now encoded id). affected #: 1 file diff -r 801e7cf8227fd2b9294a6140d0580b3c78f705fe -r 78a3508c456296bd7bd578f5c8dd121d7206fef8 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -168,7 +168,12 @@ @web.expose def errors( self, trans, id ): - hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) + try: + hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) + except: + hda = None + if not hda: + hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( trans.security.decode_id( id ) ) if not hda or not self._can_access_dataset( trans, hda ): return trans.show_error_message( "Either this dataset does not exist or you do not have permission to access it." ) return trans.fill_template( "dataset/errors.mako", hda=hda ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: When creating a new visualization for a dataset, default to dataset's dbkey.
by Bitbucket 06 Dec '12

06 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/449f0ed92b46/ changeset: 449f0ed92b46 user: jgoecks date: 2012-12-06 22:13:56 summary: When creating a new visualization for a dataset, default to dataset's dbkey. affected #: 1 file diff -r e20afb791a6685c40440743a5973ff17ba90e875 -r 449f0ed92b4621093d2e1b38dee5894f2a9b959e lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -691,25 +691,33 @@ Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`. """ + # Get dataset to add. + new_dataset_id = kwargs.get( "dataset_id", None ) + # Set up new browser if no id provided. if not id: + # Use dbkey from dataset to be added or from incoming parameter. + dbkey = None + if new_dataset_id: + dbkey = self.get_dataset( trans, new_dataset_id ).dbkey + if dbkey == '?': + dbkey = kwargs.get( "dbkey", None ) + return trans.fill_template( "tracks/browser.mako", config={}, - add_dataset=kwargs.get("dataset_id", None), - default_dbkey=kwargs.get("dbkey", None) ) + add_dataset=new_dataset_id, + default_dbkey=dbkey ) # Display saved visualization. vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True ) viz_config = self.get_visualization_config( trans, vis ) - # Get new dataset if specified. - new_dataset = kwargs.get("dataset_id", None) ''' FIXME: if new_dataset is not None: if trans.security.decode_id(new_dataset) in [ d["dataset_id"] for d in viz_config.get("tracks") ]: new_dataset = None # Already in browser, so don't add ''' - return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset ) + return trans.fill_template( 'tracks/browser.mako', config=viz_config, add_dataset=new_dataset_id ) @web.expose def circster( self, trans, id=None, hda_ldda=None, dataset_id=None, dbkey=None ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Add needed imports that went away after removing 'import *'
by Bitbucket 06 Dec '12

06 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/e20afb791a66/ changeset: e20afb791a66 user: jgoecks date: 2012-12-06 20:38:49 summary: Add needed imports that went away after removing 'import *' affected #: 2 files diff -r c0b5edcce53c541c8eaf3a2f80390c84b1f721fb -r e20afb791a6685c40440743a5973ff17ba90e875 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -1,4 +1,4 @@ -from sqlalchemy import desc +from sqlalchemy import desc, and_ from galaxy import model, web from galaxy.web import error, url_for from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings diff -r c0b5edcce53c541c8eaf3a2f80390c84b1f721fb -r e20afb791a6685c40440743a5973ff17ba90e875 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -1,10 +1,11 @@ from __future__ import absolute_import -from sqlalchemy import desc +from sqlalchemy import desc, or_, and_ from galaxy import model, web from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin from galaxy.web.framework.helpers import time_ago, grids, iff +from galaxy.util.json import from_json_string from galaxy.util.sanitize_html import sanitize_html from galaxy.visualization.genomes import decode_dbkey from galaxy.visualization.genome.visual_analytics import get_dataset_job Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add care in handling information retrieved from the tool shed by Galaxy.
by Bitbucket 06 Dec '12

06 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c0b5edcce53c/ changeset: c0b5edcce53c user: greg date: 2012-12-06 15:38:14 summary: Add care in handling information retrieved from the tool shed by Galaxy. affected #: 1 file diff -r 9cf72c86ee4f37c9035cdc30912b4f33a0f6b3bb -r c0b5edcce53c541c8eaf3a2f80390c84b1f721fb lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1099,7 +1099,12 @@ filtered_repo_info_dicts = [] for repo_info_dict in repo_info_dicts: for name, repo_info_tuple in repo_info_dict.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + # Take care in handling the repo_info_tuple as it evolves over time as new features are introduced. + if len( repo_info_tuple ) == 6: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple + repository_dependencies = None + elif len( repo_info_tuple ) == 7: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) ) relative_install_dir = os.path.join( clone_dir, name ) # Make sure the repository was not already installed. @@ -1208,7 +1213,11 @@ repo_info_dict = repo_info_dicts[ 0 ] name = repo_info_dict.keys()[ 0 ] repo_info_tuple = repo_info_dict[ name ] - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + if len( repo_info_tuple ) == 6: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple + repository_dependencies = None + elif len( repo_info_tuple ) == 7: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple url = url_join( tool_shed_url, 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \ ( name, repository_owner, changeset_revision ) ) @@ -1396,7 +1405,11 @@ # Handle case where the repository was previously installed using an older changeset_revsion, but later the repository was updated # in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one # that was previously installed. We'll look in the database instead of on disk since the repository may be uninstalled. - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple + if len( repo_info_tuple ) == 6: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple + repository_dependencies = None + elif len( repo_info_tuple ) == 7: + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) # Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset # revision to see if it was previously installed using one of them. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: A few fixes for retriveingdictionary entries and a few enhancements to the tool shed containers.
by Bitbucket 05 Dec '12

05 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9cf72c86ee4f/ changeset: 9cf72c86ee4f user: greg date: 2012-12-06 00:14:10 summary: A few fixes for retriveingdictionary entries and a few enhancements to the tool shed containers. affected #: 3 files diff -r 75a97c971d36599955f67384b6f36ca73a80dd2e -r 9cf72c86ee4f37c9035cdc30912b4f33a0f6b3bb lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -819,7 +819,6 @@ """Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config.""" repository_dependencies_tups = [] error_message = '' - config_file_name = strip_path( repository_dependencies_config ) try: # Make sure we're looking at a valid repository_dependencies.xml file. tree = util.parse_xml( repository_dependencies_config ) @@ -838,15 +837,13 @@ changeset_revision = repository_elem.attrib[ 'changeset_revision' ] user = None repository = None - # Repository dependencies are currentlhy supported only within a single tool shed. if tool_shed_is_this_tool_shed( toolshed ): try: user = sa_session.query( app.model.User ) \ .filter( app.model.User.table.c.username == owner ) \ .one() except Exception, e: - error_message = "Invalid owner %s defined for repository %s in config file %s. " % ( owner, name, config_file_name ) - error_message += "Repository dependencies will be ignored." + error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) log.debug( error_message ) return metadata_dict, error_message if user: @@ -856,8 +853,7 @@ app.model.Repository.table.c.user_id == user.id ) ) \ .first() except: - error_message = "Invalid name %s or owner %s defined for repository in config file %s. " % ( name, owner, config_file_name ) - error_message += "Repository dependencies will be ignored." + error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) log.debug( error_message ) return metadata_dict, error_message if repository: @@ -865,16 +861,19 @@ if repository_dependencies_tup not in repository_dependencies_tups: repository_dependencies_tups.append( repository_dependencies_tup ) else: - error_message = "Invalid name %s or owner %s defined for repository in config file %s. " % ( name, owner, config_file_name ) - error_message += "Repository dependencies will be ignored." + error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) log.debug( error_message ) return metadata_dict, error_message else: - # We have an invalid repository owner defined for an entry in repository_dependencies.xml. - config_file_name = strip_path( repository_dependencies_config ) - error_message = "Invalid username %s defined for owner of repository %s in config file %s. Repository dependencies will be ignored." % ( owner, name, config_file_name ) + error_message = "Invalid owner %s defined for owner of repository %s. Repository dependencies will be ignored." % ( owner, name ) log.debug( error_message ) - return metadata_dict, error_message + return metadata_dict, error_message + else: + # Repository dependencies are currentlhy supported within a single tool shed. + error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name ) + error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored." + log.debug( error_message ) + return metadata_dict, error_message if repository_dependencies_tups: repository_dependencies_dict = dict( description=root.get( 'description' ), repository_dependencies=repository_dependencies_tups ) diff -r 75a97c971d36599955f67384b6f36ca73a80dd2e -r 9cf72c86ee4f37c9035cdc30912b4f33a0f6b3bb lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -7,10 +7,11 @@ class Folder( object ): """Container object.""" - def __init__( self, id=None, key=None, label=None ): + def __init__( self, id=None, key=None, label=None, parent=None ): self.id = id self.key = key self.label = label + self.parent = parent self.description = None self.datatypes = [] self.folders = [] @@ -25,8 +26,18 @@ if folder == contained_folder: return index, contained_folder return 0, None + def contains_repository_dependency( self, repository_dependency ): + listified_repository_dependency = repository_dependency.listify + for contained_repository_dependency in self.repository_dependencies: + if contained_repository_dependency.listify == listified_repository_dependency: + return True + return False def remove_repository_dependency( self, repository_dependency ): - self.repository_dependencies.remove( repository_dependency ) + listified_repository_dependency = repository_dependency.listify + for contained_repository_dependency in self.repository_dependencies: + if contained_repository_dependency.listify == listified_repository_dependency: + self.repository_dependencies.remove( contained_repository_dependency ) + class Datatype( object ): """Datatype object""" def __init__( self, id=None, extension=None, type=None, mimetype=None, subclass=None ): @@ -102,9 +113,9 @@ if datatypes: datatype_id = 0 folder_id += 1 - datatypes_root_folder = Folder( id=folder_id, key='root', label='root' ) + datatypes_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 - folder = Folder( id=folder_id, key='datatypes', label=label ) + folder = Folder( id=folder_id, key='datatypes', label=label, parent=datatypes_root_folder ) datatypes_root_folder.folders.append( folder ) # Insert a header row. datatype_id += 1 @@ -131,9 +142,9 @@ if invalid_tool_configs: invalid_tool_id = 0 folder_id += 1 - invalid_tools_root_folder = Folder( id=folder_id, key='root', label='root' ) + invalid_tools_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 - folder = Folder( id=folder_id, key='invalid_tools', label=label ) + folder = Folder( id=folder_id, key='invalid_tools', label=label, parent=invalid_tools_root_folder ) invalid_tools_root_folder.folders.append( folder ) for invalid_tool_config in invalid_tool_configs: invalid_tool_id += 1 @@ -155,24 +166,22 @@ multiple_readme_files = len( readme_files_dict ) > 1 readme_id = 0 folder_id += 1 - readme_files_root_folder = Folder( id=folder_id, key='root', label='root' ) + readme_files_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) if multiple_readme_files: folder_id += 1 - readme_files_folder = Folder( id=folder_id, key='readme_files', label=label ) + readme_files_folder = Folder( id=folder_id, key='readme_files', label=label, parent=readme_files_root_folder ) readme_files_root_folder.folders.append( readme_files_folder ) for readme_file_name, readme_file_text in readme_files_dict.items(): readme_id += 1 - readme = ReadMe( id=readme_id, - name=readme_file_name, - text=readme_file_text ) + readme = ReadMe( id=readme_id, name=readme_file_name, text=readme_file_text ) if multiple_readme_files: folder_id += 1 - folder = Folder( id=folder_id, key=readme.name, label=readme.name ) + folder = Folder( id=folder_id, key=readme.name, label=readme.name, parent=readme_files_folder ) folder.readme_files.append( readme ) readme_files_folder.folders.append( folder ) else: folder_id += 1 - readme_files_folder = Folder( id=folder_id, key='readme_files', label=readme.name ) + readme_files_folder = Folder( id=folder_id, key='readme_files', label=readme.name, parent=readme_files_root_folder ) readme_files_folder.readme_files.append( readme ) readme_files_root_folder.folders.append( readme_files_folder ) else: @@ -185,11 +194,11 @@ repository_dependency_id = 0 folder_id += 1 # Create the root folder. - repository_dependencies_root_folder = Folder( id=folder_id, key='root', label='root' ) + repository_dependencies_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 # Create the Repository dependencies folder and add it to the root folder. repository_dependencies_folder_key = repository_dependencies[ 'root_key' ] - repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label ) + repository_dependencies_folder = Folder( id=folder_id, key=repository_dependencies_folder_key, label=label, parent=repository_dependencies_root_folder ) # The received repository_dependencies is a dictionary with a single 'description' key, and one or more repository_dependency keys. # We want the description value associated with the repository_dependencies_folder. repository_dependencies_folder.description = repository_dependencies.get( 'description', None ) @@ -203,7 +212,7 @@ # Create a new folder. folder_id += 1 label = generate_repository_dependencies_folder_label_from_key( repository_name, repository_owner, changeset_revision, key ) - folder = Folder( id=folder_id, key=key, label=label ) + folder = Folder( id=folder_id, key=key, label=label, parent=repository_dependencies_folder ) for repository_dependency_tup in val: toolshed, name, owner, changeset_revision = repository_dependency_tup # Create a new repository_dependency. @@ -218,8 +227,8 @@ if not get_folder( repository_dependencies_folder, key ): # Insert the folder into the list. repository_dependencies_folder.folders.append( folder ) - # Remove repository_dependencies that are also folders. - remove_unwanted_repository_dependencies( repository_dependencies_folder ) + # Remove repository_dependencies that are also folders, and coerce empty folders into repository dependencies. + prune_repository_dependencies( repository_dependencies_folder, repository_dependencies_folder ) else: repository_dependencies_root_folder = None return folder_id, repository_dependencies_root_folder @@ -228,9 +237,9 @@ if tool_dicts: tool_id = 0 folder_id += 1 - tools_root_folder = Folder( id=folder_id, key='root', label='root' ) + tools_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 - folder = Folder( id=folder_id, key='tools', label=label ) + folder = Folder( id=folder_id, key='tools', label=label, parent=tools_root_folder ) tools_root_folder.folders.append( folder ) # Insert a header row. tool_id += 1 @@ -272,9 +281,9 @@ if tool_dependencies: tool_dependency_id = 0 folder_id += 1 - tool_dependencies_root_folder = Folder( id=folder_id, key='root', label='root' ) + tool_dependencies_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 - folder = Folder( id=folder_id, key='tool_dependencies', label=label ) + folder = Folder( id=folder_id, key='tool_dependencies', label=label, parent=tool_dependencies_root_folder ) tool_dependencies_root_folder.folders.append( folder ) # Insert a header row. tool_dependency_id += 1 @@ -320,9 +329,9 @@ if workflows: workflow_id = 0 folder_id += 1 - workflows_root_folder = Folder( id=folder_id, key='root', label='root' ) + workflows_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) folder_id += 1 - folder = Folder( id=folder_id, key='workflows', label=label ) + folder = Folder( id=folder_id, key='workflows', label=label, parent=workflows_root_folder ) workflows_root_folder.folders.append( folder ) # Insert a header row. workflow_id += 1 @@ -388,10 +397,19 @@ def key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, key ): toolshed_base_url, key_name, key_owner, key_changeset_revision = get_components_from_key( key ) return repository_name == key_name and repository_owner == key_owner and changeset_revision == key_changeset_revision -def remove_unwanted_repository_dependencies( folder ): +def prune_folder( folder, repository_dependency, key ): + if get_folder( folder, key ): + folder.remove_repository_dependency( repository_dependency ) + for sub_folder in folder.folders: + prune_folder( sub_folder, repository_dependency, key ) +def prune_repository_dependencies( folder, root_folder ): + """Remove repository_dependencies that are also folders, and coerce empty folders into repository dependencies.""" + remove_repository_dependencies( folder, root_folder ) + for sub_folder in folder.folders: + prune_repository_dependencies( sub_folder, root_folder ) +def remove_repository_dependencies( folder, root_folder ): for repository_dependency in folder.repository_dependencies: toolshed, name, owner, changeset_revision = repository_dependency.listify key = generate_repository_dependencies_key_for_repository( toolshed, name, owner, changeset_revision ) - if get_folder( folder, key ): - folder.remove_repository_dependency( repository_dependency ) + prune_folder( root_folder, repository_dependency, key ) \ No newline at end of file diff -r 75a97c971d36599955f67384b6f36ca73a80dd2e -r 9cf72c86ee4f37c9035cdc30912b4f33a0f6b3bb lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1066,10 +1066,10 @@ raw_text = response.read() response.close() repo_information_dict = from_json_string( raw_text ) - includes_tools = util.string_as_bool( repo_information_dict[ 'includes_tools' ] ) - includes_repository_dependencies = util.string_as_bool( repo_information_dict[ 'includes_repository_dependencies' ] ) - includes_tool_dependencies = util.string_as_bool( repo_information_dict[ 'includes_tool_dependencies' ] ) - encoded_repo_info_dicts = util.listify( repo_information_dict[ 'repo_info_dicts' ] ) + includes_tools = util.string_as_bool( repo_information_dict.get( 'includes_tools', False ) ) + includes_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_repository_dependencies', False ) ) + includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) + encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) ) repo_info_dicts = [ tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] if ( not includes_tools and not includes_repository_dependencies ) or \ ( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Allow matching in tool_handlers and tool_runners on toolshed guid, toolshed guid minus version, and based (old) id. Matching occurs in that order (more specific IDs override less specific ones).
by Bitbucket 05 Dec '12

05 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/75a97c971d36/ changeset: 75a97c971d36 user: natefoo date: 2012-12-05 23:50:23 summary: Allow matching in tool_handlers and tool_runners on toolshed guid, toolshed guid minus version, and based (old) id. Matching occurs in that order (more specific IDs override less specific ones). affected #: 1 file diff -r 42a6e3f82c0d2c5ec5bd4af1fca3bac125ffe9c9 -r 75a97c971d36599955f67384b6f36ca73a80dd2e lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -993,17 +993,24 @@ else: self.parallelism = None # Set job handler(s). Each handler is a dict with 'url' and, optionally, 'params'. - self_id = self.id.lower() + self_ids = [ self.id.lower() ] + if self.old_id != self.id: + # Handle toolshed guids + self_ids = [ self.id.lower(), self.id.lower().rsplit('/',1)[0], self.old_id.lower() ] self.job_handlers = [ { "name" : name } for name in self.app.config.default_job_handlers ] # Set custom handler(s) if they're defined. - if self_id in self.app.config.tool_handlers: - self.job_handlers = self.app.config.tool_handlers[ self_id ] + for self_id in self_ids: + if self_id in self.app.config.tool_handlers: + self.job_handlers = self.app.config.tool_handlers[ self_id ] + break # Set job runner(s). Each runner is a dict with 'url' and, optionally, 'params'. # Set job runner to the cluster default self.job_runners = [ { "url" : self.app.config.default_cluster_job_runner } ] # Set custom runner(s) if they're defined. - if self_id in self.app.config.tool_runners: - self.job_runners = self.app.config.tool_runners[ self_id ] + for self_id in self_ids: + if self_id in self.app.config.tool_runners: + self.job_runners = self.app.config.tool_runners[ self_id ] + break # Is this a 'hidden' tool (hidden in tool menu) self.hidden = util.xml_text(root, "hidden") if self.hidden: self.hidden = util.string_as_bool(self.hidden) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 05 Dec '12

05 Dec '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8ea1787b037b/ changeset: 8ea1787b037b user: inithello date: 2012-12-05 20:36:20 summary: More tool shed functional test enhancements. affected #: 21 files diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/base/common.py --- /dev/null +++ b/test/tool_shed/base/common.py @@ -0,0 +1,15 @@ +admin_user = None +admin_user_private_role = None +admin_email = 'test(a)bx.psu.edu' +admin_username = 'admin-user' + +test_user_1 = None +test_user_1_private_role = None +test_user_1_email = 'test-1(a)bx.psu.edu' +test_user_1_name = 'user1' + +new_repository_dependencies_xml = '''<?xml version="1.0"?> +<repositories> + <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}" /> +</repositories> +''' diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1,6 +1,7 @@ from base.twilltestcase import * from galaxy.webapps.community.util.hgweb_config import * from test_db_util import * +from common import * import string from galaxy import eggs @@ -137,6 +138,10 @@ tc.fv( "1", "selected_files_to_delete", ','.join( files_to_delete ) ) tc.submit( 'select_files_to_delete_button' ) self.check_for_strings( strings_displayed, strings_not_displayed ) + def display_manage_repository_page( 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 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 ) @@ -204,6 +209,15 @@ else: string = string.replace( character, replacement ) return string + def generate_repository_dependency_xml( self, repository, xml_filename ): + changeset_revision = self.get_repository_tip( repository ) + template_parser = string.Template( new_repository_dependencies_xml ) + repository_dependency_xml = template_parser.safe_substitute( toolshed_url=self.url, + owner=repository.user.username, + repository_name=repository.name, + changeset_revision=changeset_revision ) + # Save the generated xml to test-data/emboss_5/repository_dependencies.xml. + file( xml_filename, 'w' ).write( repository_dependency_xml ) def get_latest_repository_metadata_for_repository( self, repository ): # TODO: This will not work as expected. Fix it. return repository.metadata_revisions[ 0 ] @@ -279,10 +293,6 @@ ( self.security.encode_id( repository.id ), tool_xml_path, changeset_revision ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def display_manage_repository_page( 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 revoke_write_access( self, repository, username ): url = '/repository/manage_repository?user_access_button=Remove&id=%s&remove_auth=%s' % \ ( self.security.encode_id( repository.id ), username ) diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/functional/test_0000_basic_repository_features.py --- a/test/tool_shed/functional/test_0000_basic_repository_features.py +++ b/test/tool_shed/functional/test_0000_basic_repository_features.py @@ -1,16 +1,6 @@ from tool_shed.base.twilltestcase import * from tool_shed.base.test_db_util import * -admin_user = None -admin_user_private_role = None -admin_email = 'test(a)bx.psu.edu' -admin_username = 'admin-user' - -test_user_1 = None -test_user_1_private_role = None -test_user_1_email = 'test-1(a)bx.psu.edu' -test_user_1_name = 'user1' - repository_name = 'filtering' repository_description = "Galaxy's filtering tool" repository_long_description = "Long description of Galaxy's filtering tool" @@ -60,7 +50,7 @@ def test_0030_upload_filtering_1_1_0( self ): """Upload filtering_1.1.0.tar to the repository""" repository = get_repository_by_name_and_owner( repository_name, admin_username ) - self.upload_file( repository, 'filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) + self.upload_file( repository, 'filtering/filtering_1.1.0.tar', commit_message="Uploaded filtering 1.1.0" ) def test_0035_verify_repository( self ): '''Display basic repository pages''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) @@ -102,7 +92,7 @@ '''Upload filtering.txt file associated with tool version 1.1.0.''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.upload_file( repository, - 'filtering.txt', + 'filtering/filtering.txt', commit_message="Uploaded filtering.txt", uncompress_file='No', remove_repo_files_not_in_tar='No' ) @@ -110,7 +100,7 @@ def test_0055_upload_filtering_test_data( self ): '''Upload filtering test data.''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) - self.upload_file( repository, 'filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' ) + self.upload_file( repository, 'filtering/filtering_test_data.tar', commit_message="Uploaded filtering test data", remove_repo_files_not_in_tar='No' ) self.display_repository_file_contents( repository=repository, filename='1.bed', filepath='test-data', @@ -121,7 +111,7 @@ '''Upload filtering version 2.2.0''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.upload_file( repository, - 'filtering_2.2.0.tar', + 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' ) def test_0065_verify_filtering_repository( self ): diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -1,16 +1,6 @@ from tool_shed.base.twilltestcase import * from tool_shed.base.test_db_util import * -admin_user = None -admin_user_private_role = None -admin_email = 'test(a)bx.psu.edu' -admin_username = 'admin-user' - -test_user_1 = None -test_user_1_private_role = None -test_user_1_email = 'test-1(a)bx.psu.edu' -test_user_1_name = 'user1' - repository_name = 'freebayes' repository_description = "Galaxy's freebayes tool" repository_long_description = "Long description of Galaxy's freebayes tool" @@ -24,11 +14,11 @@ 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_categories( self ): - """Create categories""" + def test_0005_create_category( self ): + """Create SNP Analysis category.""" self.create_category( 'SNP Analysis', 'Tools for single nucleotide polymorphism data such as WGA' ) - def test_0005_create_freebayes_repository_and_upload_tool_xml( self ): - '''Upload freebayes.xml without tool_data_table_conf.xml.sample. This should result in an error and invalid tool.''' + def test_0010_create_freebayes_repository_and_upload_tool_xml( self ): + '''Create freebayes repository and upload freebayes.xml without tool_data_table_conf.xml.sample. This should result in an error message and invalid tool.''' self.create_repository( repository_name, repository_description, repository_long_description=repository_long_description, @@ -45,38 +35,42 @@ self.check_repository_invalid_tools_for_changeset_revision( repository, tip, strings_displayed=[ 'requires an entry', 'tool_data_table_conf.xml' ] ) - def test_0010_upload_missing_tool_data_table_conf_file( self ): + def test_0015_upload_missing_tool_data_table_conf_file( self ): '''Upload the missing tool_data_table_conf.xml.sample file to the repository.''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.upload_file( repository, 'freebayes/tool_data_table_conf.xml.sample', + valid_tools_only=False, strings_displayed=[], commit_message='Uploaded the tool data table sample file.' ) - def test_0015_upload_missing_sample_loc_file( self ): + self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] ) + tip = self.get_repository_tip( repository ) + self.check_repository_invalid_tools_for_changeset_revision( repository, + tip, + strings_displayed=[ 'refers to a file', 'sam_fa_indices.loc' ] ) + def test_0020_upload_missing_sample_loc_file( self ): '''Upload the missing sam_fa_indices.loc.sample file to the repository.''' - # Freebayes does not generate an error when the loc file is missing. - # TODO: Generate a test case for that situation. repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.upload_file( repository, 'freebayes/sam_fa_indices.loc.sample', strings_displayed=[], commit_message='Uploaded tool data table .loc file.' ) - def test_0020_upload_invalid_tool_dependency_xml( self ): + def test_0025_upload_invalid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.5 of the freebayes package.''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.upload_file( repository, - os.path.join( 'freebayes', 'invalid_deps', 'tool_dependencies.xml' ), + os.path.join( 'freebayes', 'invalid_tool_dependencies', 'tool_dependencies.xml' ), strings_displayed=[ 'Name, version and type from a tool requirement tag does not match' ], commit_message='Uploaded invalid tool dependency XML.' ) - def test_0025_upload_valid_tool_dependency_xml( self ): + def test_0030_upload_valid_tool_dependency_xml( self ): '''Upload tool_dependencies.xml defining version 0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8 of the freebayes package.''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.upload_file( repository, os.path.join( 'freebayes', 'tool_dependencies.xml' ), commit_message='Uploaded valid tool dependency XML.' ) - def test_0030_verify_tool_dependencies( self ): + def test_0035_verify_tool_dependencies( self ): '''Verify that the uploaded tool_dependencies.xml specifies the correct package versions.''' repository = get_repository_by_name_and_owner( repository_name, admin_username ) self.display_manage_repository_page( repository, - strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools' ], - strings_not_displayed=[ 'Invalid tools' ] ) + strings_displayed=[ 'freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Valid tools' ], + strings_not_displayed=[ 'Invalid tools' ] ) diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/functional/test_0020_basic_repository_dependencies.py --- /dev/null +++ b/test/tool_shed/functional/test_0020_basic_repository_dependencies.py @@ -0,0 +1,71 @@ +from tool_shed.base.twilltestcase import * +from tool_shed.base.test_db_util import * + +datatypes_repository_name = 'emboss_datatypes' +datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." +datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." + +emboss_repository_name = 'emboss_5' +emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' +emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' + +class TestBasicRepositoryDependencies( ShedTwillTestCase ): + '''Testing emboss 5 with repository dependencies.''' + def test_0000_initiate_users( self ): + """Create necessary user accounts and login as an admin 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 ) + self.logout() + self.login( email=test_user_1_email, username=test_user_1_name ) + test_user_1 = get_user( test_user_1_email ) + assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email + test_user_1_private_role = get_private_role( test_user_1 ) + def test_0005_create_category( self ): + """Create Sequence Analysis category""" + self.logout() + self.login( email=admin_email, username=admin_username ) + self.create_category( 'Sequence Analysis', 'Tools for performing Protein and DNA/RNA analysis' ) + def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): + '''Create and populate the emboss_datatypes repository.''' + self.logout() + self.login( email=test_user_1_email, username=test_user_1_name ) + self.create_repository( datatypes_repository_name, + datatypes_repository_description, + repository_long_description=datatypes_repository_long_description, + categories=[ 'Sequence Analysis' ], + strings_displayed=[] ) + repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) + self.upload_file( repository, 'emboss/datatypes/datatypes_conf.xml', commit_message='Uploaded datatypes_conf.xml.' ) + def test_0015_verify_datatypes_in_datatypes_repository( self ): + '''Verify that the emboss_datatypes repository contains datatype entries.''' + repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) + self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) + def test_0020_create_emboss_5_repository_and_upload_files( self ): + '''Create and populate the emboss_5 repository.''' + self.create_repository( emboss_repository_name, + emboss_repository_description, + repository_long_description=emboss_repository_long_description, + categories=[ 'Text Manipulation' ], + strings_displayed=[] ) + repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name ) + self.upload_file( repository, 'emboss/5/emboss.tar', commit_message='Uploaded emboss_5.tar' ) + def test_0025_generate_and_upload_repository_dependencies_xml( self ): + '''Generate and upload the repository_dependencies.xml file''' + repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name ) + datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) + self.generate_repository_dependency_xml( datatypes_repository, self.get_filename( 'emboss/5/repository_dependencies.xml' ) ) + self.upload_file( repository, 'emboss/5/repository_dependencies.xml', commit_message='Uploaded repository_dependencies.xml' ) + def test_0030_verify_emboss_5_repository_dependency_on_emboss_datatypes( self ): + '''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.''' + repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name ) + datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) + changeset_revision = self.get_repository_tip( datatypes_repository ) + strings_displayed = [ datatypes_repository_name, test_user_1_name, changeset_revision, 'Repository dependencies' ] + self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) + def test_0035_cleanup( self ): + '''Clean up generated test data.''' + if os.path.exists( self.get_filename( 'emboss/5/repository_dependencies.xml' ) ): + os.remove( self.get_filename( 'emboss/5/repository_dependencies.xml' ) ) diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/functional/test_0020_emboss_repository_dependencies.py --- a/test/tool_shed/functional/test_0020_emboss_repository_dependencies.py +++ /dev/null @@ -1,95 +0,0 @@ -from tool_shed.base.twilltestcase import * -from tool_shed.base.test_db_util import * - -admin_user = None -admin_user_private_role = None -admin_email = 'test(a)bx.psu.edu' -admin_username = 'admin-user' - -test_user_1 = None -test_user_1_private_role = None -test_user_1_email = 'test-1(a)bx.psu.edu' -test_user_1_name = 'user1' - -datatypes_repository_name = 'emboss_datatypes' -datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools." -datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools." - -emboss_repository_name = 'emboss_5' -emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' -emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools' - -new_repository_dependencies_xml = '''<?xml version="1.0"?> -<repositories> - <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}" /> -</repositories> -''' - -class TestEmbossRepositoryDependencies( ShedTwillTestCase ): - '''Testing emboss 5 with repository dependencies.''' - def test_0000_initiate_users( self ): - """Create necessary user accounts and login as an admin 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 ) - self.logout() - self.login( email=test_user_1_email, username=test_user_1_name ) - test_user_1 = get_user( test_user_1_email ) - assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % regular_email - test_user_1_private_role = get_private_role( test_user_1 ) - def test_0005_create_categories( self ): - """Create categories""" - self.logout() - self.login( email=admin_email, username=admin_username ) - self.create_category( 'Sequence Analysis', 'Tools for performing Protein and DNA/RNA analysis' ) - def test_0010_create_emboss_datatypes_repository_and_upload_tarball( self ): - '''Create the emboss_datatypes repository and upload the tarball.''' - self.logout() - self.login( email=test_user_1_email, username=test_user_1_name ) - self.create_repository( datatypes_repository_name, - datatypes_repository_description, - repository_long_description=datatypes_repository_long_description, - categories=[ 'Sequence Analysis' ], - strings_displayed=[] ) - repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) - self.upload_file( repository, - 'emboss_5/datatypes_conf.xml', - commit_message='Uploaded datatypes_conf.xml.' ) - def test_0015_verify_datatypes_in_datatypes_repository( self ): - '''Verify that the emboss_datatypes repository contains datatype entries.''' - repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) - self.display_manage_repository_page( repository, strings_displayed=[ 'Datatypes', 'equicktandem', 'hennig86', 'vectorstrip' ] ) - def test_0020_generate_repository_dependencies_xml( self ): - '''Generate the repository_dependencies.xml file for the emboss_5 repository.''' - datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) - changeset_revision = self.get_repository_tip( datatypes_repository ) - template_parser = string.Template( new_repository_dependencies_xml ) - repository_dependency_xml = template_parser.safe_substitute( toolshed_url=self.url, - owner=test_user_1_name, - repository_name=datatypes_repository.name, - changeset_revision=changeset_revision ) - # Save the generated xml to test-data/emboss_5/repository_dependencies.xml. - file( self.get_filename( 'emboss_5/repository_dependencies.xml' ), 'w' ).write( repository_dependency_xml ) - def test_0025_create_emboss_5_repository_and_upload_files( self ): - '''Create the emboss_5 repository and upload a tool tarball, then generate and upload repository_dependencies.xml.''' - self.create_repository( emboss_repository_name, - emboss_repository_description, - repository_long_description=emboss_repository_long_description, - categories=[ 'Text Manipulation' ], - strings_displayed=[] ) - repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name ) - self.upload_file( repository, 'emboss_5/emboss_5.tar', commit_message='Uploaded emboss_5.tar' ) - self.upload_file( repository, 'emboss_5/repository_dependencies.xml', commit_message='Uploaded repository_dependencies.xml' ) - def test_0030_verify_emboss_5_repository_dependency_on_emboss_datatypes( self ): - '''Verify that the emboss_5 repository now depends on the emboss_datatypes repository with correct name, owner, and changeset revision.''' - repository = get_repository_by_name_and_owner( emboss_repository_name, test_user_1_name ) - datatypes_repository = get_repository_by_name_and_owner( datatypes_repository_name, test_user_1_name ) - changeset_revision = self.get_repository_tip( datatypes_repository ) - strings_displayed = [ datatypes_repository_name, test_user_1_name, changeset_revision, 'Repository dependencies' ] - self.display_manage_repository_page( repository, strings_displayed=strings_displayed ) - def test_0035_cleanup( self ): - '''Clean up generated test data.''' - if os.path.exists( self.get_filename( 'emboss_5/repository_dependencies.xml' ) ): - os.remove( self.get_filename( 'emboss_5/repository_dependencies.xml' ) ) diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/emboss/5/emboss.tar Binary file test/tool_shed/test_data/emboss/5/emboss.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/emboss/6/emboss.tar Binary file test/tool_shed/test_data/emboss/6/emboss.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml --- /dev/null +++ b/test/tool_shed/test_data/emboss/datatypes/datatypes_conf.xml @@ -0,0 +1,101 @@ +<?xml version="1.0"?> +<datatypes> + <registration> + <datatype extension="acedb" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="asn1" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="btwisted" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="cai" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="charge" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="checktrans" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="chips" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="clustal" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="codata" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="codcmp" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="coderet" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="compseq" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="cpgplot" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="cpgreport" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="cusp" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="cut" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="dan" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="dbmotif" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="diffseq" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="digest" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="dreg" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="einverted" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="embl" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="epestfind" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="equicktandem" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="est2genome" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="etandem" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="excel" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="feattable" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="fitch" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="freak" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="fuzztran" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="garnier" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="gcg" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="geecee" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="genbank" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="hmoment" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="isochore" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="markx0" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="markx1" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="markx10" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="markx2" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="markx3" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="match" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="mega" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="meganon" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="motif" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="msf" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="nametable" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="ncbi" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="needle" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="nexus" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="nexusnon" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="noreturn" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="pair" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="palindrome" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="pepcoil" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="pepinfo" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="pepstats" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="phylip" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="phylipnon" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="pir" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="polydot" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="preg" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="prettyseq" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="primersearch" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="regions" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="score" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="selex" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="seqtable" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="showfeat" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="showorf" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="simple" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="sixpack" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="srs" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="srspair" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="staden" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="strider" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="supermatcher" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="swiss" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="syco" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="table" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="tagseq" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="textsearch" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="wobble" type="galaxy.datatypes.data:Text" subclass="True"/> + <datatype extension="wordcount" type="galaxy.datatypes.data:Text" subclass="True"/> + </registration> +</datatypes> diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/emboss_5/datatypes_conf.xml --- a/test/tool_shed/test_data/emboss_5/datatypes_conf.xml +++ /dev/null @@ -1,101 +0,0 @@ -<?xml version="1.0"?> -<datatypes> - <registration> - <datatype extension="acedb" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="asn1" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="btwisted" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="cai" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="charge" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="checktrans" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="chips" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="clustal" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="codata" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="codcmp" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="coderet" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="compseq" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="cpgplot" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="cpgreport" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="cusp" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="cut" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="dan" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="dbmotif" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="diffseq" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="digest" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="dreg" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="einverted" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="embl" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="epestfind" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="equicktandem" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="est2genome" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="etandem" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="excel" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="feattable" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="fitch" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="freak" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="fuzznuc" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="fuzzpro" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="fuzztran" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="garnier" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="gcg" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="geecee" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="genbank" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="helixturnhelix" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="hennig86" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="hmoment" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="ig" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="isochore" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="jackknifer" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="jackknifernon" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="markx0" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="markx1" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="markx10" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="markx2" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="markx3" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="match" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="mega" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="meganon" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="motif" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="msf" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="nametable" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="ncbi" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="needle" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="newcpgreport" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="newcpgseek" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="nexus" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="nexusnon" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="noreturn" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="pair" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="palindrome" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="pepcoil" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="pepinfo" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="pepstats" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="phylip" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="phylipnon" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="pir" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="polydot" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="preg" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="prettyseq" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="primersearch" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="regions" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="score" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="selex" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="seqtable" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="showfeat" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="showorf" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="simple" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="sixpack" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="srs" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="srspair" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="staden" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="strider" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="supermatcher" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="swiss" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="syco" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="table" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="tagseq" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="textsearch" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="vectorstrip" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="wobble" type="galaxy.datatypes.data:Text" subclass="True"/> - <datatype extension="wordcount" type="galaxy.datatypes.data:Text" subclass="True"/> - </registration> -</datatypes> diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/emboss_5/emboss_5.tar Binary file test/tool_shed/test_data/emboss_5/emboss_5.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/filtering.txt --- a/test/tool_shed/test_data/filtering.txt +++ /dev/null @@ -1,1 +0,0 @@ -Readme file for filtering 1.1.0 diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/filtering/filtering.txt --- /dev/null +++ b/test/tool_shed/test_data/filtering/filtering.txt @@ -0,0 +1,1 @@ +Readme file for filtering 1.1.0 diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/filtering/filtering_1.1.0.tar Binary file test/tool_shed/test_data/filtering/filtering_1.1.0.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/filtering/filtering_2.2.0.tar Binary file test/tool_shed/test_data/filtering/filtering_2.2.0.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/filtering/filtering_test_data.tar Binary file test/tool_shed/test_data/filtering/filtering_test_data.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/filtering_1.1.0.tar Binary file test/tool_shed/test_data/filtering_1.1.0.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/filtering_2.2.0.tar Binary file test/tool_shed/test_data/filtering_2.2.0.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/filtering_test_data.tar Binary file test/tool_shed/test_data/filtering_test_data.tar has changed diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/freebayes/invalid_deps/tool_dependencies.xml --- a/test/tool_shed/test_data/freebayes/invalid_deps/tool_dependencies.xml +++ /dev/null @@ -1,46 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="freebayes" version="0.9.5"> - <install version="1.0"> - <actions> - <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> - <action type="shell_command">git reset --hard 9696d0ce8a962f7bb61c4791be5ce44312b81cf8</action> - <action type="shell_command">make</action> - <action type="move_directory_files"> - <source_directory>bin</source_directory> - <destination_directory>$INSTALL_DIR/bin</destination_directory> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -FreeBayes requires g++ and the standard C and C++ development libraries. -Additionally, cmake is required for building the BamTools API. - </readme> - </package> - <package name="samtools" version="0.2.15"> - <install version="1.0"> - <actions> - <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> - <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>samtools</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>misc/maq2sam-long</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme> -Compiling SAMtools requires the ncurses and zlib development libraries. - </readme> - </package> -</tool_dependency> diff -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml --- /dev/null +++ b/test/tool_shed/test_data/freebayes/invalid_tool_dependencies/tool_dependencies.xml @@ -0,0 +1,46 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="freebayes" version="0.9.5"> + <install version="1.0"> + <actions> + <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action> + <action type="shell_command">git reset --hard 9696d0ce8a962f7bb61c4791be5ce44312b81cf8</action> + <action type="shell_command">make</action> + <action type="move_directory_files"> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR/bin</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +FreeBayes requires g++ and the standard C and C++ development libraries. +Additionally, cmake is required for building the BamTools API. + </readme> + </package> + <package name="samtools" version="0.2.15"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> + <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>samtools</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>misc/maq2sam-long</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +Compiling SAMtools requires the ncurses and zlib development libraries. + </readme> + </package> +</tool_dependency> https://bitbucket.org/galaxy/galaxy-central/changeset/42a6e3f82c0d/ changeset: 42a6e3f82c0d user: inithello date: 2012-12-05 20:37:48 summary: Fix error in tool xml dynamic options parsing. affected #: 1 file diff -r 8ea1787b037bf957535d39ab1c834a241bb2a5e5 -r 42a6e3f82c0d2c5ec5bd4af1fca3bac125ffe9c9 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -8,6 +8,7 @@ from galaxy.webapps.community.util.container_util import * from galaxy.datatypes.checkers import * from galaxy.model.orm import * +from galaxy.tools.parameters import dynamic_options from galaxy import eggs import pkg_resources @@ -249,7 +250,7 @@ if isinstance( input_param, parameters.basic.SelectToolParameter ) and input_param.is_dynamic: # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist. options = input_param.dynamic_options or input_param.options - if options: + if options and isinstance( options, dynamic_options.DynamicOptions ): if options.tool_data_table or options.missing_tool_data_table_name: # Make sure the repository contains a tool_data_table_conf.xml.sample file. sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Handle invalid repository dependency definitions.
by Bitbucket 05 Dec '12

05 Dec '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1b6819e4598d/ changeset: 1b6819e4598d user: greg date: 2012-12-05 17:46:36 summary: Handle invalid repository dependency definitions. affected #: 2 files diff -r 1b8fd73e2a5464fd2caab261dbf10017f119185d -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -618,7 +618,7 @@ message = '' if not displaying_invalid_tool: if metadata_dict: - message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip( trans.app ) ) + message += "Metadata may have been defined for some items in revision '%s'. " % str( repository.tip( trans.app ) ) message += "Correct the following problems if necessary and reset metadata.%s" % new_line else: message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip( trans.app ) ) @@ -719,7 +719,9 @@ # See if we have a repository dependencies defined. if name == 'repository_dependencies.xml': path_to_repository_dependencies_config = os.path.join( root, name ) - metadata_dict = generate_repository_dependency_metadata( path_to_repository_dependencies_config, metadata_dict ) + metadata_dict, error_message = generate_repository_dependency_metadata( app, path_to_repository_dependencies_config, metadata_dict ) + if error_message: + invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = get_relative_path_to_repository_file( root, @@ -812,29 +814,71 @@ if requirements_dict: tool_dependencies_dict[ dependency_key ] = requirements_dict return tool_dependencies_dict -def generate_repository_dependency_metadata( repository_dependencies_config, metadata_dict ): +def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict ): + """Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config.""" repository_dependencies_tups = [] + error_message = '' + config_file_name = strip_path( repository_dependencies_config ) try: # Make sure we're looking at a valid repository_dependencies.xml file. tree = util.parse_xml( repository_dependencies_config ) root = tree.getroot() is_valid = root.tag == 'repositories' except Exception, e: - log.debug( "Error parsing %s, exception: %s" % ( repository_dependencies_config, str( e ) ) ) + error_message = "Error parsing %s, exception: %s" % ( repository_dependencies_config, str( e ) ) + log.debug( error_message ) is_valid = False if is_valid: + sa_session = app.model.context.current for repository_elem in root.findall( 'repository' ): - 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 ) + toolshed = repository_elem.attrib[ 'toolshed' ] + name = repository_elem.attrib[ 'name' ] + owner = repository_elem.attrib[ 'owner'] + changeset_revision = repository_elem.attrib[ 'changeset_revision' ] + user = None + repository = None + # Repository dependencies are currentlhy supported only within a single tool shed. + if tool_shed_is_this_tool_shed( toolshed ): + try: + user = sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.username == owner ) \ + .one() + except Exception, e: + error_message = "Invalid owner %s defined for repository %s in config file %s. " % ( owner, name, config_file_name ) + error_message += "Repository dependencies will be ignored." + log.debug( error_message ) + return metadata_dict, error_message + if user: + try: + repository = sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.name == name, + app.model.Repository.table.c.user_id == user.id ) ) \ + .first() + except: + error_message = "Invalid name %s or owner %s defined for repository in config file %s. " % ( name, owner, config_file_name ) + error_message += "Repository dependencies will be ignored." + log.debug( error_message ) + return metadata_dict, error_message + if repository: + repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + if repository_dependencies_tup not in repository_dependencies_tups: + repository_dependencies_tups.append( repository_dependencies_tup ) + else: + error_message = "Invalid name %s or owner %s defined for repository in config file %s. " % ( name, owner, config_file_name ) + error_message += "Repository dependencies will be ignored." + log.debug( error_message ) + return metadata_dict, error_message + else: + # We have an invalid repository owner defined for an entry in repository_dependencies.xml. + config_file_name = strip_path( repository_dependencies_config ) + error_message = "Invalid username %s defined for owner of repository %s in config file %s. Repository dependencies will be ignored." % ( owner, name, config_file_name ) + log.debug( error_message ) + return metadata_dict, error_message if repository_dependencies_tups: repository_dependencies_dict = dict( description=root.get( 'description' ), repository_dependencies=repository_dependencies_tups ) metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict - return metadata_dict + return metadata_dict, error_message def generate_tool_dependency_metadata( app, repository, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository, diff -r 1b8fd73e2a5464fd2caab261dbf10017f119185d -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -38,7 +38,7 @@ self.upload_file( repository, 'freebayes/freebayes.xml', valid_tools_only=False, - strings_displayed=[ 'Metadata was defined', 'This file requires an entry', 'tool_data_table_conf' ], + strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ], commit_message='Uploaded the tool xml.' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] ) tip = self.get_repository_tip( repository ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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