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[galaxyproject/usegalaxy-playbook] c571cd: Update Test.
by GitHub 24 Sep '14

24 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c571cd114dac2da43631ee10ae510064c501b373 https://github.com/galaxyproject/usegalaxy-playbook/commit/c571cd114dac2da4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7aed3778587e/ Changeset: 7aed3778587e Branch: next-stable User: jmchilton Date: 2014-09-24 19:21:44+00:00 Summary: Allow remotely executed tools to write version files to the temp directory. Like with discovered datasets - such use of this directory should be phased out in favor of the job's working directory of a job relative to it. Affected #: 1 file diff -r 381c547b681aa09fccab1b03963377115d9d7cc4 -r 7aed3778587ed9d8e703721adc0f8e4df656e902 lib/galaxy/webapps/galaxy/api/job_files.py --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -118,9 +118,16 @@ https://gist.github.com/jmchilton/9103619.) """ in_work_dir = self.__in_working_directory( job, path, trans.app ) - if not in_work_dir and not self.__is_output_dataset_path( job, path ): + allow_temp_dir_file = self.__is_allowed_temp_dir_file( trans.app, job, path ) + if not in_work_dir and not allow_temp_dir_file and not self.__is_output_dataset_path( job, path ): raise exceptions.ItemAccessibilityException("Job is not authorized to write to supplied path.") + def __is_allowed_temp_dir_file( self, app, job, path ): + # grrr.. need to get away from new_file_path - these should be written + # to job working directory like metadata files. + in_temp_dir = util.in_directory( path, app.config.new_file_path ) + return in_temp_dir and os.path.split( path )[ -1 ].startswith( "GALAXY_VERSION_") + def __is_output_dataset_path( self, job, path ): """ Check if is an output path for this job or a file in the an output's extra files path. https://bitbucket.org/galaxy/galaxy-central/commits/5296d69134bd/ Changeset: 5296d69134bd Branch: next-stable User: jmchilton Date: 2014-09-24 19:21:44+00:00 Summary: Rework version command to work with job wrappers that have not had 'prepare' executed. Traditionally all synchronous job wrappers have had 'prepare' called when they are queued up, but prepare isn't called on the more transient job wrappers that are created in response to Pulsar asnchronous status update messages. Affected #: 1 file diff -r 7aed3778587ed9d8e703721adc0f8e4df656e902 -r 5296d69134bddeb11246c70347d83c6073da646f lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1035,7 +1035,7 @@ else: final_job_state = job.states.ERROR - if self.write_version_cmd: + if self.tool.version_string_cmd: version_filename = self.get_version_string_path() if os.path.exists(version_filename): self.version_string = open(version_filename).read() https://bitbucket.org/galaxy/galaxy-central/commits/583d9ba9c4f9/ Changeset: 583d9ba9c4f9 User: jmchilton Date: 2014-09-24 19:23:08+00:00 Summary: Merge next-stable. Affected #: 2 files diff -r fda2251972f612ded8c3c5cb096795ace194d192 -r 583d9ba9c4f9673c42f4378829b741845e95f1c0 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1035,7 +1035,7 @@ else: final_job_state = job.states.ERROR - if self.write_version_cmd: + if self.tool.version_string_cmd: version_filename = self.get_version_string_path() if os.path.exists(version_filename): self.version_string = open(version_filename).read() diff -r fda2251972f612ded8c3c5cb096795ace194d192 -r 583d9ba9c4f9673c42f4378829b741845e95f1c0 lib/galaxy/webapps/galaxy/api/job_files.py --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -118,9 +118,16 @@ https://gist.github.com/jmchilton/9103619.) """ in_work_dir = self.__in_working_directory( job, path, trans.app ) - if not in_work_dir and not self.__is_output_dataset_path( job, path ): + allow_temp_dir_file = self.__is_allowed_temp_dir_file( trans.app, job, path ) + if not in_work_dir and not allow_temp_dir_file and not self.__is_output_dataset_path( job, path ): raise exceptions.ItemAccessibilityException("Job is not authorized to write to supplied path.") + def __is_allowed_temp_dir_file( self, app, job, path ): + # grrr.. need to get away from new_file_path - these should be written + # to job working directory like metadata files. + in_temp_dir = util.in_directory( path, app.config.new_file_path ) + return in_temp_dir and os.path.split( path )[ -1 ].startswith( "GALAXY_VERSION_") + def __is_output_dataset_path( self, job, path ): """ Check if is an output path for this job or a file in the an output's extra files path. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: History panel: allow toggling show_hidden/deleted without altering the sessionStorage preferences
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fda2251972f6/ Changeset: fda2251972f6 User: carlfeberhard Date: 2014-09-24 18:54:33+00:00 Summary: History panel: allow toggling show_hidden/deleted without altering the sessionStorage preferences Affected #: 6 files diff -r 139468c177324ecce07469265692988e92fb3842 -r fda2251972f612ded8c3c5cb096795ace194d192 client/galaxy/scripts/mvc/history/history-panel-edit.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js @@ -284,7 +284,6 @@ view.$el.slideDown( panel.fxSpeed ); }, - /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */ _getItemViewOptions : function( model ){ var options = _super.prototype._getItemViewOptions.call( this, model ); @@ -301,7 +300,7 @@ * @param {Model} the item model to check */ _handleHdaDeletionChange : function( itemModel ){ - if( itemModel.get( 'deleted' ) && !this.storage.get( 'show_deleted' ) ){ + if( itemModel.get( 'deleted' ) && !this.showDeleted ){ this.removeItemView( itemModel ); } }, @@ -310,7 +309,7 @@ * @param {Model} the item model to check */ _handleHdaVisibleChange : function( itemModel ){ - if( itemModel.hidden() && !this.storage.get( 'show_hidden' ) ){ + if( itemModel.hidden() && !this.storage.showHidden ){ this.removeItemView( itemModel ); } }, diff -r 139468c177324ecce07469265692988e92fb3842 -r fda2251972f612ded8c3c5cb096795ace194d192 client/galaxy/scripts/mvc/history/history-panel.js --- a/client/galaxy/scripts/mvc/history/history-panel.js +++ b/client/galaxy/scripts/mvc/history/history-panel.js @@ -254,6 +254,10 @@ _setUpWebStorage : function( initiallyExpanded, show_deleted, show_hidden ){ //if( !this.model ){ return this; } //this.log( '_setUpWebStorage', initiallyExpanded, show_deleted, show_hidden ); + if( this.storage ){ + this.stopListening( this.storage ); + } + this.storage = new HistoryPrefs({ id: HistoryPrefs.historyStorageKey( this.model.get( 'id' ) ) }); @@ -276,6 +280,18 @@ this.trigger( 'new-storage', this.storage, this ); this.log( this + ' (init\'d) storage:', this.storage.get() ); + + this.listenTo( this.storage, { + 'change:show_deleted' : function( view, newVal ){ + this.showDeleted = newVal; + }, + 'change:show_hidden' : function( view, newVal ){ + this.showHidden = newVal; + } + }, this ); + this.showDeleted = ( show_deleted !== undefined )? show_deleted : this.storage.get( 'show_deleted' ); + this.showHidden = ( show_hidden !== undefined )? show_hidden : this.storage.get( 'show_hidden' ); + return this; }, @@ -317,8 +333,8 @@ _filterItem : function( model ){ var panel = this; return ( _super.prototype._filterItem.call( panel, model ) - && ( !model.hidden() || panel.storage.get( 'show_hidden' ) ) - && ( !model.isDeletedOrPurged() || panel.storage.get( 'show_deleted' ) ) ); + && ( !model.hidden() || panel.showHidden ) + && ( !model.isDeletedOrPurged() || panel.showDeleted ) ); }, /** in this override, add a linktarget, and expand if id is in web storage */ @@ -372,12 +388,16 @@ * (2) re-rendering the history * @returns {Boolean} new show_deleted setting */ - toggleShowDeleted : function( show ){ - show = ( show !== undefined )?( show ):( !this.storage.get( 'show_deleted' ) ); - this.storage.set( 'show_deleted', show ); + toggleShowDeleted : function( show, store ){ + show = ( show !== undefined )?( show ):( !this.showDeleted ); + store = ( store !== undefined )?( store ):( true ); + this.showDeleted = show; + if( store ){ + this.storage.set( 'show_deleted', show ); + } //TODO:?? to events on storage('change:show_deleted') this.renderItems(); - return this.storage.get( 'show_deleted' ); + return this.showDeleted; }, /** Handle the user toggling the deleted visibility by: @@ -385,12 +405,16 @@ * (2) re-rendering the history * @returns {Boolean} new show_hidden setting */ - toggleShowHidden : function( show ){ - show = ( show !== undefined )?( show ):( !this.storage.get( 'show_hidden' ) ); - this.storage.set( 'show_hidden', show ); - //TODO:?? to events on storage('change:show_hidden') + toggleShowHidden : function( show, store ){ + show = ( show !== undefined )?( show ):( !this.showHidden ); + store = ( store !== undefined )?( store ):( true ); + this.showHidden = show; + if( store ){ + this.storage.set( 'show_hidden', show ); + } + //TODO:?? to events on storage('change:show_deleted') this.renderItems(); - return this.storage.get( 'show_hidden' ); + return this.showHidden; }, /** On the first search, if there are no details - load them, then search */ diff -r 139468c177324ecce07469265692988e92fb3842 -r fda2251972f612ded8c3c5cb096795ace194d192 static/scripts/mvc/history/history-panel-edit.js --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -284,7 +284,6 @@ view.$el.slideDown( panel.fxSpeed ); }, - /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */ _getItemViewOptions : function( model ){ var options = _super.prototype._getItemViewOptions.call( this, model ); @@ -301,7 +300,7 @@ * @param {Model} the item model to check */ _handleHdaDeletionChange : function( itemModel ){ - if( itemModel.get( 'deleted' ) && !this.storage.get( 'show_deleted' ) ){ + if( itemModel.get( 'deleted' ) && !this.showDeleted ){ this.removeItemView( itemModel ); } }, @@ -310,7 +309,7 @@ * @param {Model} the item model to check */ _handleHdaVisibleChange : function( itemModel ){ - if( itemModel.hidden() && !this.storage.get( 'show_hidden' ) ){ + if( itemModel.hidden() && !this.storage.showHidden ){ this.removeItemView( itemModel ); } }, diff -r 139468c177324ecce07469265692988e92fb3842 -r fda2251972f612ded8c3c5cb096795ace194d192 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -254,6 +254,10 @@ _setUpWebStorage : function( initiallyExpanded, show_deleted, show_hidden ){ //if( !this.model ){ return this; } //this.log( '_setUpWebStorage', initiallyExpanded, show_deleted, show_hidden ); + if( this.storage ){ + this.stopListening( this.storage ); + } + this.storage = new HistoryPrefs({ id: HistoryPrefs.historyStorageKey( this.model.get( 'id' ) ) }); @@ -276,6 +280,18 @@ this.trigger( 'new-storage', this.storage, this ); this.log( this + ' (init\'d) storage:', this.storage.get() ); + + this.listenTo( this.storage, { + 'change:show_deleted' : function( view, newVal ){ + this.showDeleted = newVal; + }, + 'change:show_hidden' : function( view, newVal ){ + this.showHidden = newVal; + } + }, this ); + this.showDeleted = ( show_deleted !== undefined )? show_deleted : this.storage.get( 'show_deleted' ); + this.showHidden = ( show_hidden !== undefined )? show_hidden : this.storage.get( 'show_hidden' ); + return this; }, @@ -317,8 +333,8 @@ _filterItem : function( model ){ var panel = this; return ( _super.prototype._filterItem.call( panel, model ) - && ( !model.hidden() || panel.storage.get( 'show_hidden' ) ) - && ( !model.isDeletedOrPurged() || panel.storage.get( 'show_deleted' ) ) ); + && ( !model.hidden() || panel.showHidden ) + && ( !model.isDeletedOrPurged() || panel.showDeleted ) ); }, /** in this override, add a linktarget, and expand if id is in web storage */ @@ -372,12 +388,16 @@ * (2) re-rendering the history * @returns {Boolean} new show_deleted setting */ - toggleShowDeleted : function( show ){ - show = ( show !== undefined )?( show ):( !this.storage.get( 'show_deleted' ) ); - this.storage.set( 'show_deleted', show ); + toggleShowDeleted : function( show, store ){ + show = ( show !== undefined )?( show ):( !this.showDeleted ); + store = ( store !== undefined )?( store ):( true ); + this.showDeleted = show; + if( store ){ + this.storage.set( 'show_deleted', show ); + } //TODO:?? to events on storage('change:show_deleted') this.renderItems(); - return this.storage.get( 'show_deleted' ); + return this.showDeleted; }, /** Handle the user toggling the deleted visibility by: @@ -385,12 +405,16 @@ * (2) re-rendering the history * @returns {Boolean} new show_hidden setting */ - toggleShowHidden : function( show ){ - show = ( show !== undefined )?( show ):( !this.storage.get( 'show_hidden' ) ); - this.storage.set( 'show_hidden', show ); - //TODO:?? to events on storage('change:show_hidden') + toggleShowHidden : function( show, store ){ + show = ( show !== undefined )?( show ):( !this.showHidden ); + store = ( store !== undefined )?( store ):( true ); + this.showHidden = show; + if( store ){ + this.storage.set( 'show_hidden', show ); + } + //TODO:?? to events on storage('change:show_deleted') this.renderItems(); - return this.storage.get( 'show_hidden' ); + return this.showHidden; }, /** On the first search, if there are no details - load them, then search */ diff -r 139468c177324ecce07469265692988e92fb3842 -r fda2251972f612ded8c3c5cb096795ace194d192 static/scripts/packed/mvc/history/history-panel-edit.js --- a/static/scripts/packed/mvc/history/history-panel-edit.js +++ b/static/scripts/packed/mvc/history/history-panel-edit.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","utils/localization"],function(f,h,k,d,c,g,j,a,b){var i=f.HistoryPanel;var e=i.extend({HDAViewClass:c.HDAListItemEdit,HDCAViewClass:g.HDCAListItemEdit,initialize:function(l){l=l||{};i.prototype.initialize.call(this,l);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=l.purgeAllowed||false;this.annotationEditorShown=l.annotationEditorShown||false;this.tagsEditorShown=l.tagsEditorShown||false;this.multiselectActions=l.multiselectActions||this._getActions()},_setUpCollectionListeners:function(){i.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(l){this.model.fetch()},this);return this},_setUpModelListeners:function(){i.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var l=i.prototype._buildNewRender.call(this);if(!this.model){return l}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(l);this._renderAnnotation(l)}return l},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(l.find(".controls .actions"))})},_renderAnnotation:function(l){var m=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:l.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDAAnnotationEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDAAnnotationEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(l.find(".controls .actions"))})},_setUpBehaviors:function(l){l=l||this.$el;i.prototype._setUpBehaviors.call(this,l);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new PopupMenu(l.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var m=this,n=".controls .name";l.find(n).attr("title",b("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(o){var p=m.model.get("name");if(o&&o!==p){m.$el.find(n).text(o);m.model.save({name:o}).fail(function(){m.$el.find(n).text(m.model.previous("name"))})}else{m.$el.find(n).text(p)}}})},_getActions:function(){var l=this,m=[{html:b("Hide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.hide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Unhide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.unhide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Delete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype["delete"];l.getSelectedModels().ajaxQueue(n)}},{html:b("Undelete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.undelete;l.getSelectedModels().ajaxQueue(n)}}];if(l.purgeAllowed){m.push({html:b("Permanently delete datasets"),func:function(){if(confirm(b("This will permanently remove the data in your datasets. Are you sure?"))){var n=d.HistoryDatasetAssociation.prototype.purge;l.getSelectedModels().ajaxQueue(n)}}})}m.push({html:b("Build Dataset List"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"list")}});m.push({html:b("Build Dataset Pair"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"paired")}});m.push({html:b("Build List of Dataset Pairs"),func:_.bind(l._showPairedCollectionModal,l)});return m},_showPairedCollectionModal:function(){var l=this,m=l.getSelectedModels().toJSON().filter(function(n){return n.history_content_type==="dataset"&&n.state===k.OK});if(m.length){require(["mvc/collection/paired-collection-creator"],function(n){window.creator=n.pairedCollectionCreatorModal(m,{historyId:l.model.id})})}else{}},_attachItems:function(l){this.$list(l).append(this.views.reverse().map(function(m){return m.$el}));return this},_attachView:function(m){var l=this;l.views.unshift(m);l.$list().prepend(m.render(0).$el.hide());m.$el.slideDown(l.fxSpeed)},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){if(l.get("deleted")&&!this.storage.get("show_deleted")){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){if(l.hidden()&&!this.storage.get("show_hidden")){this.removeItemView(l)}},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:e}}); \ No newline at end of file +define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","utils/localization"],function(f,h,k,d,c,g,j,a,b){var i=f.HistoryPanel;var e=i.extend({HDAViewClass:c.HDAListItemEdit,HDCAViewClass:g.HDCAListItemEdit,initialize:function(l){l=l||{};i.prototype.initialize.call(this,l);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=l.purgeAllowed||false;this.annotationEditorShown=l.annotationEditorShown||false;this.tagsEditorShown=l.tagsEditorShown||false;this.multiselectActions=l.multiselectActions||this._getActions()},_setUpCollectionListeners:function(){i.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(l){this.model.fetch()},this);return this},_setUpModelListeners:function(){i.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var l=i.prototype._buildNewRender.call(this);if(!this.model){return l}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(l);this._renderAnnotation(l)}return l},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(l.find(".controls .actions"))})},_renderAnnotation:function(l){var m=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:l.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDAAnnotationEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDAAnnotationEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(l.find(".controls .actions"))})},_setUpBehaviors:function(l){l=l||this.$el;i.prototype._setUpBehaviors.call(this,l);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new PopupMenu(l.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var m=this,n=".controls .name";l.find(n).attr("title",b("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(o){var p=m.model.get("name");if(o&&o!==p){m.$el.find(n).text(o);m.model.save({name:o}).fail(function(){m.$el.find(n).text(m.model.previous("name"))})}else{m.$el.find(n).text(p)}}})},_getActions:function(){var l=this,m=[{html:b("Hide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.hide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Unhide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.unhide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Delete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype["delete"];l.getSelectedModels().ajaxQueue(n)}},{html:b("Undelete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.undelete;l.getSelectedModels().ajaxQueue(n)}}];if(l.purgeAllowed){m.push({html:b("Permanently delete datasets"),func:function(){if(confirm(b("This will permanently remove the data in your datasets. Are you sure?"))){var n=d.HistoryDatasetAssociation.prototype.purge;l.getSelectedModels().ajaxQueue(n)}}})}m.push({html:b("Build Dataset List"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"list")}});m.push({html:b("Build Dataset Pair"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"paired")}});m.push({html:b("Build List of Dataset Pairs"),func:_.bind(l._showPairedCollectionModal,l)});return m},_showPairedCollectionModal:function(){var l=this,m=l.getSelectedModels().toJSON().filter(function(n){return n.history_content_type==="dataset"&&n.state===k.OK});if(m.length){require(["mvc/collection/paired-collection-creator"],function(n){window.creator=n.pairedCollectionCreatorModal(m,{historyId:l.model.id})})}else{}},_attachItems:function(l){this.$list(l).append(this.views.reverse().map(function(m){return m.$el}));return this},_attachView:function(m){var l=this;l.views.unshift(m);l.$list().prepend(m.render(0).$el.hide());m.$el.slideDown(l.fxSpeed)},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){if(l.get("deleted")&&!this.showDeleted){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){if(l.hidden()&&!this.storage.showHidden){this.removeItemView(l)}},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:e}}); \ No newline at end of file diff -r 139468c177324ecce07469265692988e92fb3842 -r fda2251972f612ded8c3c5cb096795ace194d192 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(d,f,l,b,a,m,g,o,e){var j=o.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpanded:function(p){var q="expandedIds";this.save(q,_.extend(this.get(q),_.object([p.id],[p.get("id")])))},removeExpanded:function(p){var q="expandedIds";this.save(q,_.omit(this.get(q),p.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});j.storageKeyPrefix="history:";j.historyStorageKey=function h(p){if(!p){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+p)}return(j.storageKeyPrefix+p)};j.get=function c(p){return new j({id:j.historyStorageKey(p)})};j.clearAll=function i(q){for(var p in sessionStorage){if(p.indexOf(j.storageKeyPrefix)===0){sessionStorage.removeItem(p)}}};var n=d.ModelListPanel;var k=n.extend({HDAViewClass:b.HDAListItemView,HDCAViewClass:a.HDCAListItemView,collectionClass:l.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:n.prototype.className+" history-panel",emptyMsg:e("This history is empty"),noneFoundMsg:e("No matching datasets found"),searchPlaceholder:e("search datasets"),initialize:function(p){n.prototype.initialize.call(this,p);this.linkTarget=p.linkTarget||"_blank"},freeModel:function(){n.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){n.prototype._setUpListeners.call(this);this.on("error",function(q,t,p,s,r){this.errorHandler(q,t,p,s,r)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(s,r,q,t){this.info("loadHistoryWithDetails:",s,r,q,t);var p=function(u){return _.values(j.get(u.id).get("expandedIds"))};return this.loadHistory(s,r,q,t,p)},loadHistory:function(t,s,r,u,p){this.info("loadHistory:",t,s,r,u,p);var q=this;s=s||{};q.trigger("loading",q);var v=f.History.getHistoryData(t,{historyFn:r,contentsFn:u,detailIdsFn:s.initiallyExpanded||p});return q._loadHistoryFromXHR(v,s).fail(function(y,w,x){q.trigger("error",q,y,s,e("An error was encountered while "+w),{historyId:t,history:x||{}})}).always(function(){q.trigger("loading-done",q)})},_loadHistoryFromXHR:function(r,q){var p=this;r.then(function(s,t){p.JSONToModel(s,t,q);p.render()});r.fail(function(t,s){p.render()});return r},refreshContents:function(q,p){if(this.model){return this.model.refresh(q,p)}return $.when()},JSONToModel:function(s,p,q){this.log("JSONToModel:",s,p,q);q=q||{};var r=new f.History(s,p,q);this.setModel(r);return r},setModel:function(q,p){p=p||{};n.prototype.setModel.call(this,q,p);if(this.model){this._setUpWebStorage(p.initiallyExpanded,p.show_deleted,p.show_hidden)}},_setUpWebStorage:function(q,p,r){this.storage=new j({id:j.historyStorageKey(this.model.get("id"))});if(_.isObject(q)){this.storage.set("expandedIds",q)}if(_.isBoolean(p)){this.storage.set("show_deleted",p)}if(_.isBoolean(r)){this.storage.set("show_hidden",r)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());return this},_buildNewRender:function(){var p=n.prototype._buildNewRender.call(this);if(this.multiselectActions.length){p.find(".controls .actions").prepend(this._renderSelectButton())}return p},_renderSelectButton:function(p){return faIconButton({title:e("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(p){var q=p.get("history_content_type");switch(q){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+q)},_filterItem:function(q){var p=this;return(n.prototype._filterItem.call(p,q)&&(!q.hidden()||p.storage.get("show_hidden"))&&(!q.isDeletedOrPurged()||p.storage.get("show_deleted")))},_getItemViewOptions:function(q){var p=n.prototype._getItemViewOptions.call(this,q);return _.extend(p,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[q.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(q){var p=this;n.prototype._setUpItemViewListeners.call(p,q);q.on("expanded",function(r){p.storage.addExpanded(r.model)});q.on("collapsed",function(r){p.storage.removeExpanded(r.model)});return this},getSelectedModels:function(){var p=n.prototype.getSelectedModels.call(this);p.historyId=this.collection.historyId;return p},events:_.extend(_.clone(n.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(p){p=(p!==undefined)?(p):(!this.storage.get("show_deleted"));this.storage.set("show_deleted",p);this.renderItems();return this.storage.get("show_deleted")},toggleShowHidden:function(p){p=(p!==undefined)?(p):(!this.storage.get("show_hidden"));this.storage.set("show_hidden",p);this.renderItems();return this.storage.get("show_hidden")},_firstSearch:function(p){var q=this,r=".history-search-input";this.log("onFirstSearch",p);if(q.model.contents.haveDetails()){q.searchItems(p);return}q.$el.find(r).searchInput("toggle-loading");q.model.contents.fetchAllDetails({silent:true}).always(function(){q.$el.find(r).searchInput("toggle-loading")}).done(function(){q.searchItems(p)})},errorHandler:function(r,u,q,t,s){this.error(r,u,q,t,s);if(u&&u.status===0&&u.readyState===0){}else{if(u&&u.status===502){}else{var p=this._parseErrorMessage(r,u,q,t,s);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",p.message,p.details)})}else{this.displayMessage("error",p.message,p.details)}}}},_parseErrorMessage:function(t,w,x,r,p,u){var s=Galaxy.currUser,v={message:this._bePolite(r),details:{message:r,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(w)?(_.omit(x,"xhr")):(x),xhr:w,source:(_.isFunction(t.toJSON))?(t.toJSON()):(t+""),user:(s instanceof g.User)?(s.toJSON()):(s+"")}};_.extend(v.details,p||{});if(w&&_.isFunction(w.getAllResponseHeaders)){var q=w.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(y){return y.split(": ")});v.details.xhr.responseHeaders=_.object(q)}return v},_bePolite:function(p){p=p||e("An error occurred while getting updates from the server");return p+". "+e("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(u,v,t){var r=this;this.scrollToTop();var s=this.$messages(),p=$("<div/>").addClass(u+"message").html(v);if(!_.isEmpty(t)){var q=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(r._messageToModalOptions(u,v,t));return false});p.append(" ",q)}return s.html(p)},_messageToModalOptions:function(s,v,r){var p=this,q={title:"Details"};if(_.isObject(r)){r=_.omit(r,_.functions(r));var u=JSON.stringify(r,null," "),t=$("<pre/>").text(u);q.body=$("<div/>").append(t)}else{q.body=$("<div/>").html(r)}q.buttons={Ok:function(){Galaxy.modal.hide();p.clearMessages()}};return q},clearMessages:function(p){$(p.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(p){return this.scrollToItem(_.first(this.viewsWhereModel({hid:p})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});k.prototype.templates=(function(){var p=o.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle">',"</div>",'<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',e("This history has been deleted"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',e("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',e("None"),"</button>","</div>",'<button class="list-action-popup-btn btn btn-default">',e("For all selected"),"...</button>","</div>","</div>"],"history");return _.extend(_.clone(n.prototype.templates),{controls:p})}());return{HistoryPanel:k}}); \ No newline at end of file +define(["mvc/list/list-panel","mvc/history/history-model","mvc/history/history-contents","mvc/history/hda-li","mvc/history/hdca-li","mvc/collection/collection-panel","mvc/user/user-model","mvc/base-mvc","utils/localization"],function(d,f,l,b,a,m,g,o,e){var j=o.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:false,show_hidden:false},addExpanded:function(p){var q="expandedIds";this.save(q,_.extend(this.get(q),_.object([p.id],[p.get("id")])))},removeExpanded:function(p){var q="expandedIds";this.save(q,_.omit(this.get(q),p.id))},toString:function(){return"HistoryPrefs("+this.id+")"}});j.storageKeyPrefix="history:";j.historyStorageKey=function h(p){if(!p){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+p)}return(j.storageKeyPrefix+p)};j.get=function c(p){return new j({id:j.historyStorageKey(p)})};j.clearAll=function i(q){for(var p in sessionStorage){if(p.indexOf(j.storageKeyPrefix)===0){sessionStorage.removeItem(p)}}};var n=d.ModelListPanel;var k=n.extend({HDAViewClass:b.HDAListItemView,HDCAViewClass:a.HDCAListItemView,collectionClass:l.HistoryContents,modelCollectionKey:"contents",tagName:"div",className:n.prototype.className+" history-panel",emptyMsg:e("This history is empty"),noneFoundMsg:e("No matching datasets found"),searchPlaceholder:e("search datasets"),initialize:function(p){n.prototype.initialize.call(this,p);this.linkTarget=p.linkTarget||"_blank"},freeModel:function(){n.prototype.freeModel.call(this);if(this.model){this.model.clearUpdateTimeout()}return this},_setUpListeners:function(){n.prototype._setUpListeners.call(this);this.on("error",function(q,t,p,s,r){this.errorHandler(q,t,p,s,r)});this.on("loading-done",function(){if(!this.views.length){this.trigger("empty-history",this)}})},loadHistoryWithDetails:function(s,r,q,t){this.info("loadHistoryWithDetails:",s,r,q,t);var p=function(u){return _.values(j.get(u.id).get("expandedIds"))};return this.loadHistory(s,r,q,t,p)},loadHistory:function(t,s,r,u,p){this.info("loadHistory:",t,s,r,u,p);var q=this;s=s||{};q.trigger("loading",q);var v=f.History.getHistoryData(t,{historyFn:r,contentsFn:u,detailIdsFn:s.initiallyExpanded||p});return q._loadHistoryFromXHR(v,s).fail(function(y,w,x){q.trigger("error",q,y,s,e("An error was encountered while "+w),{historyId:t,history:x||{}})}).always(function(){q.trigger("loading-done",q)})},_loadHistoryFromXHR:function(r,q){var p=this;r.then(function(s,t){p.JSONToModel(s,t,q);p.render()});r.fail(function(t,s){p.render()});return r},refreshContents:function(q,p){if(this.model){return this.model.refresh(q,p)}return $.when()},JSONToModel:function(s,p,q){this.log("JSONToModel:",s,p,q);q=q||{};var r=new f.History(s,p,q);this.setModel(r);return r},setModel:function(q,p){p=p||{};n.prototype.setModel.call(this,q,p);if(this.model){this._setUpWebStorage(p.initiallyExpanded,p.show_deleted,p.show_hidden)}},_setUpWebStorage:function(q,p,r){if(this.storage){this.stopListening(this.storage)}this.storage=new j({id:j.historyStorageKey(this.model.get("id"))});if(_.isObject(q)){this.storage.set("expandedIds",q)}if(_.isBoolean(p)){this.storage.set("show_deleted",p)}if(_.isBoolean(r)){this.storage.set("show_hidden",r)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get());this.listenTo(this.storage,{"change:show_deleted":function(s,t){this.showDeleted=t},"change:show_hidden":function(s,t){this.showHidden=t}},this);this.showDeleted=(p!==undefined)?p:this.storage.get("show_deleted");this.showHidden=(r!==undefined)?r:this.storage.get("show_hidden");return this},_buildNewRender:function(){var p=n.prototype._buildNewRender.call(this);if(this.multiselectActions.length){p.find(".controls .actions").prepend(this._renderSelectButton())}return p},_renderSelectButton:function(p){return faIconButton({title:e("Operations on multiple datasets"),classes:"show-selectors-btn",faIcon:"fa-check-square-o"})},_getItemViewClass:function(p){var q=p.get("history_content_type");switch(q){case"dataset":return this.HDAViewClass;case"dataset_collection":return this.HDCAViewClass}throw new TypeError("Unknown history_content_type: "+q)},_filterItem:function(q){var p=this;return(n.prototype._filterItem.call(p,q)&&(!q.hidden()||p.showHidden)&&(!q.isDeletedOrPurged()||p.showDeleted))},_getItemViewOptions:function(q){var p=n.prototype._getItemViewOptions.call(this,q);return _.extend(p,{linkTarget:this.linkTarget,expanded:!!this.storage.get("expandedIds")[q.id],hasUser:this.model.ownedByCurrUser()})},_setUpItemViewListeners:function(q){var p=this;n.prototype._setUpItemViewListeners.call(p,q);q.on("expanded",function(r){p.storage.addExpanded(r.model)});q.on("collapsed",function(r){p.storage.removeExpanded(r.model)});return this},getSelectedModels:function(){var p=n.prototype.getSelectedModels.call(this);p.historyId=this.collection.historyId;return p},events:_.extend(_.clone(n.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),toggleShowDeleted:function(p,q){p=(p!==undefined)?(p):(!this.showDeleted);q=(q!==undefined)?(q):(true);this.showDeleted=p;if(q){this.storage.set("show_deleted",p)}this.renderItems();return this.showDeleted},toggleShowHidden:function(p,q){p=(p!==undefined)?(p):(!this.showHidden);q=(q!==undefined)?(q):(true);this.showHidden=p;if(q){this.storage.set("show_hidden",p)}this.renderItems();return this.showHidden},_firstSearch:function(p){var q=this,r=".history-search-input";this.log("onFirstSearch",p);if(q.model.contents.haveDetails()){q.searchItems(p);return}q.$el.find(r).searchInput("toggle-loading");q.model.contents.fetchAllDetails({silent:true}).always(function(){q.$el.find(r).searchInput("toggle-loading")}).done(function(){q.searchItems(p)})},errorHandler:function(r,u,q,t,s){this.error(r,u,q,t,s);if(u&&u.status===0&&u.readyState===0){}else{if(u&&u.status===502){}else{var p=this._parseErrorMessage(r,u,q,t,s);if(!this.$messages().is(":visible")){this.once("rendered",function(){this.displayMessage("error",p.message,p.details)})}else{this.displayMessage("error",p.message,p.details)}}}},_parseErrorMessage:function(t,w,x,r,p,u){var s=Galaxy.currUser,v={message:this._bePolite(r),details:{message:r,raven:(window.Raven&&_.isFunction(Raven.lastEventId))?(Raven.lastEventId()):(undefined),agent:navigator.userAgent,url:(window.Galaxy)?(Galaxy.lastAjax.url):(undefined),data:(window.Galaxy)?(Galaxy.lastAjax.data):(undefined),options:(w)?(_.omit(x,"xhr")):(x),xhr:w,source:(_.isFunction(t.toJSON))?(t.toJSON()):(t+""),user:(s instanceof g.User)?(s.toJSON()):(s+"")}};_.extend(v.details,p||{});if(w&&_.isFunction(w.getAllResponseHeaders)){var q=w.getAllResponseHeaders();q=_.compact(q.split("\n"));q=_.map(q,function(y){return y.split(": ")});v.details.xhr.responseHeaders=_.object(q)}return v},_bePolite:function(p){p=p||e("An error occurred while getting updates from the server");return p+". "+e("Please contact a Galaxy administrator if the problem persists")+"."},displayMessage:function(u,v,t){var r=this;this.scrollToTop();var s=this.$messages(),p=$("<div/>").addClass(u+"message").html(v);if(!_.isEmpty(t)){var q=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(r._messageToModalOptions(u,v,t));return false});p.append(" ",q)}return s.html(p)},_messageToModalOptions:function(s,v,r){var p=this,q={title:"Details"};if(_.isObject(r)){r=_.omit(r,_.functions(r));var u=JSON.stringify(r,null," "),t=$("<pre/>").text(u);q.body=$("<div/>").append(t)}else{q.body=$("<div/>").html(r)}q.buttons={Ok:function(){Galaxy.modal.hide();p.clearMessages()}};return q},clearMessages:function(p){$(p.currentTarget).fadeOut(this.fxSpeed,function(){$(this).remove()});return this},scrollToHid:function(p){return this.scrollToItem(_.first(this.viewsWhereModel({hid:p})))},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});k.prototype.templates=(function(){var p=o.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= history.name %></div>',"</div>",'<div class="subtitle">',"</div>",'<div class="history-size"><%= history.nice_size %></div>','<div class="actions"></div>','<div class="messages">',"<% if( history.deleted ){ %>",'<div class="deleted-msg warningmessagesmall">',e("This history has been deleted"),"</div>","<% } %>","<% if( history.message ){ %>",'<div class="<%= history.message.level || "info" %>messagesmall">',"<%= history.message.text %>","</div>","<% } %>","</div>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',e("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',e("None"),"</button>","</div>",'<button class="list-action-popup-btn btn btn-default">',e("For all selected"),"...</button>","</div>","</div>"],"history");return _.extend(_.clone(n.prototype.templates),{controls:p})}());return{HistoryPanel:k}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Minor style fix
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/139468c17732/ Changeset: 139468c17732 User: guerler Date: 2014-09-24 18:55:20+00:00 Summary: ToolForm: Minor style fix Affected #: 2 files diff -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 -r 139468c177324ecce07469265692988e92fb3842 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1294,7 +1294,7 @@ .ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px} .ui-button-icon .button{margin-right:5px;margin-left:5px}.ui-button-icon .button .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px} .ui-button-icon .button.disabled{filter:alpha(opacity=65);opacity:.65;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=65);filter:alpha(opacity=65)} -.ui-button-icon-plain{border:none !important;background:none !important;height:inherit !important} +.ui-button-icon-plain{border:none !important;background:none !important;height:inherit !important;width:inherit !important;padding-right:3px !important} .ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} .ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} .ui-portlet,.ui-portlet-repeat,.ui-portlet-repeat{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title .portlet-title-text{vertical-align:middle} diff -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 -r 139468c177324ecce07469265692988e92fb3842 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -110,6 +110,8 @@ border: none !important; background: none !important; height: inherit !important; + width: inherit !important; + padding-right: 3px !important; } .ui-tabs { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Additional validation for batch mode, style fixes
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5a846bf0080b/ Changeset: 5a846bf0080b User: guerler Date: 2014-09-24 18:37:34+00:00 Summary: ToolForm: Additional validation for batch mode, style fixes Affected #: 11 files diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -32,6 +32,7 @@ console.debug('tools-jobs::submit - Submission canceled. Validation failed.'); return; } + console.log(job_def); // post job Utils.request('POST', galaxy_config.root + 'api/tools', job_def, @@ -66,27 +67,59 @@ // validation flag var valid = true; - // check inputs + // link this + var self = this; + + /** Highlight and scroll to error */ + function foundError (input_id, message) { + // get input field + var input_element = self.app.element_list[input_id]; + + // mark error + input_element.error(message || 'Please verify this parameter.'); + + // set flag + if (valid) { + // scroll to first input element + $(self.app.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + + // set error flag + valid = false; + } + } + + // counter for values declared in batch mode + var n_values = -1; + + // validation for (var job_input_id in job_inputs) { + // get current value + var input_value = job_inputs[job_input_id]; + // collect input field properties - var input = job_inputs[job_input_id]; var input_id = this.app.tree.match(job_input_id); var input_field = this.app.field_list[input_id]; - var input_element = this.app.element_list[input_id]; + var input_def = this.app.input_list[input_id]; - // check field validation - if (input && !input.optional && input_field && input_field.validate && !input_field.validate()) { - this.app.element_list[input_id].error('Please verify this parameter.'); - if (valid) { - // scroll to first input element - $(this.app.container).animate({ - scrollTop: input_element.$el.offset().top - 20 - }, 500); - - // validation failed - valid = false; + // check basic field validation + if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) { + foundError(input_id); + } + + // check if input field is in batch mode + if (input_value.batch) { + var n = input_value.values.length; + if (n_values === -1) { + n_values = n; + } else { + if (n_values !== n) { + foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); + } } } + } // return result diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 client/galaxy/scripts/mvc/tools/tools-select-dataset.js --- a/client/galaxy/scripts/mvc/tools/tools-select-dataset.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-dataset.js @@ -1,9 +1,12 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs'], function(Utils, Ui, Tabs) { +define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'mvc/tools/tools-template'], function(Utils, Ui, Tabs, ToolTemplate) { var View = Backbone.View.extend({ // initialize initialize : function(app, options) { + // configure options + this.options = options; + // link this var self = this; @@ -83,6 +86,11 @@ this.$el.append(this.select_datasets.$el); this.$el.append(this.select_collection.$el); + // check for batch mode + if (!this.options.multiple) { + this.$el.append(ToolTemplate.batchMode()); + } + // refresh view this.refresh(); diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -38,6 +38,13 @@ // return success message element return tmpl; + }, + + batchMode: function() { + return '<div class="ui-table-form-info">' + + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; } }; diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -32,6 +32,7 @@ console.debug('tools-jobs::submit - Submission canceled. Validation failed.'); return; } + console.log(job_def); // post job Utils.request('POST', galaxy_config.root + 'api/tools', job_def, @@ -66,27 +67,59 @@ // validation flag var valid = true; - // check inputs + // link this + var self = this; + + /** Highlight and scroll to error */ + function foundError (input_id, message) { + // get input field + var input_element = self.app.element_list[input_id]; + + // mark error + input_element.error(message || 'Please verify this parameter.'); + + // set flag + if (valid) { + // scroll to first input element + $(self.app.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + + // set error flag + valid = false; + } + } + + // counter for values declared in batch mode + var n_values = -1; + + // validation for (var job_input_id in job_inputs) { + // get current value + var input_value = job_inputs[job_input_id]; + // collect input field properties - var input = job_inputs[job_input_id]; var input_id = this.app.tree.match(job_input_id); var input_field = this.app.field_list[input_id]; - var input_element = this.app.element_list[input_id]; + var input_def = this.app.input_list[input_id]; - // check field validation - if (input && !input.optional && input_field && input_field.validate && !input_field.validate()) { - this.app.element_list[input_id].error('Please verify this parameter.'); - if (valid) { - // scroll to first input element - $(this.app.container).animate({ - scrollTop: input_element.$el.offset().top - 20 - }, 500); - - // validation failed - valid = false; + // check basic field validation + if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) { + foundError(input_id); + } + + // check if input field is in batch mode + if (input_value.batch) { + var n = input_value.values.length; + if (n_values === -1) { + n_values = n; + } else { + if (n_values !== n) { + foundError(input_id, 'Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>' + n + '</b> selection(s) while a previous field contains <b>' + n_values + '</b>.'); + } } } + } // return result diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 static/scripts/mvc/tools/tools-select-dataset.js --- a/static/scripts/mvc/tools/tools-select-dataset.js +++ b/static/scripts/mvc/tools/tools-select-dataset.js @@ -1,9 +1,12 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs'], function(Utils, Ui, Tabs) { +define(['utils/utils', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'mvc/tools/tools-template'], function(Utils, Ui, Tabs, ToolTemplate) { var View = Backbone.View.extend({ // initialize initialize : function(app, options) { + // configure options + this.options = options; + // link this var self = this; @@ -83,6 +86,11 @@ this.$el.append(this.select_datasets.$el); this.$el.append(this.select_collection.$el); + // check for batch mode + if (!this.options.multiple) { + this.$el.append(ToolTemplate.batchMode()); + } + // refresh view this.refresh(); diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -38,6 +38,13 @@ // return success message element return tmpl; + }, + + batchMode: function() { + return '<div class="ui-table-form-info">' + + '<i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>' + + 'This is a batch mode input field. A separate job will be triggered for each dataset.' + '</div>'; } }; diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var g in h){var f=h[g];if(!f){f="Please verify this parameter."}c.app.element_list[g].error(f)}}})},_validation:function(h){var e=h.inputs;var g=true;for(var j in e){var d=e[j];var f=this.app.tree.match(j);var c=this.app.field_list[f];var i=this.app.element_list[f];if(d&&!d.optional&&c&&c.validate&&!c.validate()){this.app.element_list[f].error("Please verify this parameter.");if(g){$(this.app.container).animate({scrollTop:i.$el.offset().top-20},500);g=false}}}return g},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.log(d);b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var g in h){var f=h[g];if(!f){f="Please verify this parameter."}c.app.element_list[g].error(f)}}})},_validation:function(h){var e=h.inputs;var c=true;var o=this;function m(n,p){var q=o.app.element_list[n];q.error(p||"Please verify this parameter.");if(c){$(o.app.container).animate({scrollTop:q.$el.offset().top-20},500);c=false}}var l=-1;for(var k in e){var f=e[k];var j=this.app.tree.match(k);var d=this.app.field_list[j];var i=this.app.input_list[j];if(i&&!i.optional&&d&&d.validate&&!d.validate()){m(j)}if(f.batch){var g=f.values.length;if(l===-1){l=g}else{if(l!==g){m(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+g+"</b> selection(s) while a previous field contains <b>"+l+"</b>.")}}}}return c},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 static/scripts/packed/mvc/tools/tools-select-dataset.js --- a/static/scripts/packed/mvc/tools/tools-select-dataset.js +++ b/static/scripts/packed/mvc/tools/tools-select-dataset.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs"],function(b,d,a){var c=Backbone.View.extend({initialize:function(m,g){var f=this;this.setElement("<div/>");this.current="hda";this.button_new=new d.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});var k=m.datasets.filterType({content_type:"dataset",data_types:g.extensions});var j=[];for(var h in k){j.push({label:k[h].get("name"),value:k[h].get("id")})}this.select_datasets=new d.Select.View({multiple:true,data:j,value:j[0]&&j[0].value,onchange:function(){f.trigger("change")}});var l=m.datasets.filterType({content_type:"collection",data_types:g.extensions});var e=[];for(var h in l){e.push({label:l[h].get("name"),value:l[h].get("id")})}this.select_collection=new d.Select.View({data:e,value:e[0]&&e[0].value,onchange:function(){f.trigger("change")}});this.$el.append(b.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},value:function(){var f=null;switch(this.current){case"hda":f=this.select_datasets;break;case"hdca":f=this.select_collection;break}var h=f.value();if(!(h instanceof Array)){h=[h]}var e={batch:!this.options.multiple,values:[]};for(var g in h){e.values.push({id:h[g],src:this.current})}return e},validate:function(){switch(this.current){case"hda":return this.select_datasets.validate();case"hdca":return this.select_collection.validate()}},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(n,h){this.options=h;var g=this;this.setElement("<div/>");this.current="hda";this.button_new=new e.RadioButton.View({value:this.current,data:[{icon:"fa-file-o",label:"Select datasets",value:"hda"},{icon:"fa-files-o",label:"Select a collection",value:"hdca"}],onchange:function(i){g.current=i;g.refresh();g.trigger("change")}});var l=n.datasets.filterType({content_type:"dataset",data_types:h.extensions});var k=[];for(var j in l){k.push({label:l[j].get("name"),value:l[j].get("id")})}this.select_datasets=new e.Select.View({multiple:true,data:k,value:k[0]&&k[0].value,onchange:function(){g.trigger("change")}});var m=n.datasets.filterType({content_type:"collection",data_types:h.extensions});var f=[];for(var j in m){f.push({label:m[j].get("name"),value:m[j].get("id")})}this.select_collection=new e.Select.View({data:f,value:f[0]&&f[0].value,onchange:function(){g.trigger("change")}});this.$el.append(c.wrap(this.button_new.$el));this.$el.append(this.select_datasets.$el);this.$el.append(this.select_collection.$el);if(!this.options.multiple){this.$el.append(a.batchMode())}this.refresh();this.on("change",function(){if(h.onchange){h.onchange(g.value())}})},value:function(){var g=null;switch(this.current){case"hda":g=this.select_datasets;break;case"hdca":g=this.select_collection;break}var j=g.value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple,values:[]};for(var h in j){f.values.push({id:j[h],src:this.current})}return f},validate:function(){switch(this.current){case"hda":return this.select_datasets.validate();case"hdca":return this.select_collection.validate()}},refresh:function(){switch(this.current){case"hda":this.select_datasets.$el.fadeIn();this.select_collection.$el.hide();break;case"hdca":this.select_datasets.$el.hide();this.select_collection.$el.fadeIn();break}}});return{View:d}}); \ No newline at end of file diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1294,7 +1294,7 @@ .ui-button-icon{margin-right:5px}.ui-button-icon ul i{font-size:1.2em;margin-right:5px;position:relative;top:1px} .ui-button-icon .button{margin-right:5px;margin-left:5px}.ui-button-icon .button .title{position:relative;font-size:0.8em;font-weight:normal;top:-1px} .ui-button-icon .button.disabled{filter:alpha(opacity=65);opacity:.65;-ms-filter:progid:DXImageTransform.Microsoft.Alpha(Opacity=65);filter:alpha(opacity=65)} -.ui-button-icon-plain{border:none !important;background:none !important} +.ui-button-icon-plain{border:none !important;background:none !important;height:inherit !important} .ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} .ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} .ui-portlet,.ui-portlet-repeat,.ui-portlet-repeat{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title .portlet-title-text{vertical-align:middle} diff -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec -r 5a846bf0080bc7db4b7d99e9f6046182fbff8ec5 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -109,6 +109,7 @@ &:extend(.icon-btn); border: none !important; background: none !important; + height: inherit !important; } .ui-tabs { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/381c547b681a/ Changeset: 381c547b681a Branch: next-stable User: carlfeberhard Date: 2014-09-24 17:54:04+00:00 Summary: Fix to 83aaac5: copy changes into client/ Affected #: 3 files diff -r 83aaac537783198aa18da52e0bccc31018ef968a -r 381c547b681aa09fccab1b03963377115d9d7cc4 client/galaxy/scripts/galaxy.frame.js --- a/client/galaxy/scripts/galaxy.frame.js +++ b/client/galaxy/scripts/galaxy.frame.js @@ -73,8 +73,59 @@ }); this._refresh(); }, + + /** + * Add a dataset to the frames. + */ + add_dataset: function(dataset_id) { + var self = this; + require(['mvc/data'], function(DATA) { + var dataset = new DATA.Dataset({ id: dataset_id }); + $.when( dataset.fetch() ).then( function() { + // Construct frame config based on dataset's type. + var frame_config = { + title: dataset.get('name') + }, + // HACK: For now, assume 'tabular' and 'interval' are the only + // modules that contain tabular files. This needs to be replaced + // will a is_datatype() function. + is_tabular = _.find(['tabular', 'interval'], function(data_type) { + return dataset.get('data_type').indexOf(data_type) !== -1; + }); + + // Use tabular chunked display if dataset is tabular; otherwise load via URL. + if (is_tabular) { + var tabular_dataset = new DATA.TabularDataset(dataset.toJSON()); + _.extend(frame_config, { + type: 'other', + content: function( parent_elt ) { + DATA.createTabularDatasetChunkedView({ + model: tabular_dataset, + parent_elt: parent_elt, + embedded: true, + height: '100%' + }); + } + }); + } + else { + _.extend(frame_config, { + type: 'url', + content: galaxy_config.root + 'datasets/' + + dataset.id + '/display/?preview=True' + }); + } + + self.add(frame_config); + + }); + }); + + }, - // adds and displays a new frame/window + /** + * Add and display a new frame/window based on options. + */ add: function(options) { // open new tab diff -r 83aaac537783198aa18da52e0bccc31018ef968a -r 381c547b681aa09fccab1b03963377115d9d7cc4 client/galaxy/scripts/mvc/data.js --- a/client/galaxy/scripts/mvc/data.js +++ b/client/galaxy/scripts/mvc/data.js @@ -20,7 +20,11 @@ }, initialize: function() { - this._set_metadata(); + // Metadata can be passed in as a model or a set of attributes; if it's + // already a model, there's no need to set metadata. + if (!this.get('metadata')) { + this._set_metadata(); + } // Update metadata on change. this.on('change', this._set_metadata, this); diff -r 83aaac537783198aa18da52e0bccc31018ef968a -r 381c547b681aa09fccab1b03963377115d9d7cc4 client/galaxy/scripts/mvc/dataset/dataset-li.js --- a/client/galaxy/scripts/mvc/dataset/dataset-li.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js @@ -161,24 +161,8 @@ var self = this; displayBtnData.onclick = function( ev ){ if( Galaxy.frame && Galaxy.frame.active ){ - // Create frame with TabularChunkedView. - Galaxy.frame.add({ - title : "Data Viewer: " + self.model.get( 'name' ), - type : "other", - content : function( parent_elt ){ - require(['mvc/data'], function(DATA) { - var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) }); - $.when( new_dataset.fetch() ).then( function(){ - DATA.createTabularDatasetChunkedView({ - model: new_dataset, - parent_elt: parent_elt, - embedded: true, - height: '100%' - }); - }); - }); - } - }); + // Add dataset to frames. + Galaxy.frame.add_dataset(self.model.get('id')); ev.preventDefault(); } }; https://bitbucket.org/galaxy/galaxy-central/commits/7d53a4a090a4/ Changeset: 7d53a4a090a4 User: carlfeberhard Date: 2014-09-24 17:54:22+00:00 Summary: Merge default Affected #: 3 files diff -r 5808dd487257734f138833d5eed4d6a2d7e42f30 -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec client/galaxy/scripts/galaxy.frame.js --- a/client/galaxy/scripts/galaxy.frame.js +++ b/client/galaxy/scripts/galaxy.frame.js @@ -73,8 +73,59 @@ }); this._refresh(); }, + + /** + * Add a dataset to the frames. + */ + add_dataset: function(dataset_id) { + var self = this; + require(['mvc/data'], function(DATA) { + var dataset = new DATA.Dataset({ id: dataset_id }); + $.when( dataset.fetch() ).then( function() { + // Construct frame config based on dataset's type. + var frame_config = { + title: dataset.get('name') + }, + // HACK: For now, assume 'tabular' and 'interval' are the only + // modules that contain tabular files. This needs to be replaced + // will a is_datatype() function. + is_tabular = _.find(['tabular', 'interval'], function(data_type) { + return dataset.get('data_type').indexOf(data_type) !== -1; + }); + + // Use tabular chunked display if dataset is tabular; otherwise load via URL. + if (is_tabular) { + var tabular_dataset = new DATA.TabularDataset(dataset.toJSON()); + _.extend(frame_config, { + type: 'other', + content: function( parent_elt ) { + DATA.createTabularDatasetChunkedView({ + model: tabular_dataset, + parent_elt: parent_elt, + embedded: true, + height: '100%' + }); + } + }); + } + else { + _.extend(frame_config, { + type: 'url', + content: galaxy_config.root + 'datasets/' + + dataset.id + '/display/?preview=True' + }); + } + + self.add(frame_config); + + }); + }); + + }, - // adds and displays a new frame/window + /** + * Add and display a new frame/window based on options. + */ add: function(options) { // open new tab diff -r 5808dd487257734f138833d5eed4d6a2d7e42f30 -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec client/galaxy/scripts/mvc/data.js --- a/client/galaxy/scripts/mvc/data.js +++ b/client/galaxy/scripts/mvc/data.js @@ -20,7 +20,11 @@ }, initialize: function() { - this._set_metadata(); + // Metadata can be passed in as a model or a set of attributes; if it's + // already a model, there's no need to set metadata. + if (!this.get('metadata')) { + this._set_metadata(); + } // Update metadata on change. this.on('change', this._set_metadata, this); diff -r 5808dd487257734f138833d5eed4d6a2d7e42f30 -r 7d53a4a090a4b17ea46a256b4dc16712297d48ec client/galaxy/scripts/mvc/dataset/dataset-li.js --- a/client/galaxy/scripts/mvc/dataset/dataset-li.js +++ b/client/galaxy/scripts/mvc/dataset/dataset-li.js @@ -161,24 +161,8 @@ var self = this; displayBtnData.onclick = function( ev ){ if( Galaxy.frame && Galaxy.frame.active ){ - // Create frame with TabularChunkedView. - Galaxy.frame.add({ - title : "Data Viewer: " + self.model.get( 'name' ), - type : "other", - content : function( parent_elt ){ - require(['mvc/data'], function(DATA) { - var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) }); - $.when( new_dataset.fetch() ).then( function(){ - DATA.createTabularDatasetChunkedView({ - model: new_dataset, - parent_elt: parent_elt, - embedded: true, - height: '100%' - }); - }); - }); - } - }); + // Add dataset to frames. + Galaxy.frame.add_dataset(self.model.get('id')); ev.preventDefault(); } }; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Merge next-stable to default.
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5808dd487257/ Changeset: 5808dd487257 User: jgoecks Date: 2014-09-24 17:47:53+00:00 Summary: Merge next-stable to default. Affected #: 6 files diff -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f -r 5808dd487257734f138833d5eed4d6a2d7e42f30 static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -73,8 +73,59 @@ }); this._refresh(); }, + + /** + * Add a dataset to the frames. + */ + add_dataset: function(dataset_id) { + var self = this; + require(['mvc/data'], function(DATA) { + var dataset = new DATA.Dataset({ id: dataset_id }); + $.when( dataset.fetch() ).then( function() { + // Construct frame config based on dataset's type. + var frame_config = { + title: dataset.get('name') + }, + // HACK: For now, assume 'tabular' and 'interval' are the only + // modules that contain tabular files. This needs to be replaced + // will a is_datatype() function. + is_tabular = _.find(['tabular', 'interval'], function(data_type) { + return dataset.get('data_type').indexOf(data_type) !== -1; + }); + + // Use tabular chunked display if dataset is tabular; otherwise load via URL. + if (is_tabular) { + var tabular_dataset = new DATA.TabularDataset(dataset.toJSON()); + _.extend(frame_config, { + type: 'other', + content: function( parent_elt ) { + DATA.createTabularDatasetChunkedView({ + model: tabular_dataset, + parent_elt: parent_elt, + embedded: true, + height: '100%' + }); + } + }); + } + else { + _.extend(frame_config, { + type: 'url', + content: galaxy_config.root + 'datasets/' + + dataset.id + '/display/?preview=True' + }); + } + + self.add(frame_config); + + }); + }); + + }, - // adds and displays a new frame/window + /** + * Add and display a new frame/window based on options. + */ add: function(options) { // open new tab diff -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f -r 5808dd487257734f138833d5eed4d6a2d7e42f30 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -20,7 +20,11 @@ }, initialize: function() { - this._set_metadata(); + // Metadata can be passed in as a model or a set of attributes; if it's + // already a model, there's no need to set metadata. + if (!this.get('metadata')) { + this._set_metadata(); + } // Update metadata on change. this.on('change', this._set_metadata, this); diff -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f -r 5808dd487257734f138833d5eed4d6a2d7e42f30 static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -161,24 +161,8 @@ var self = this; displayBtnData.onclick = function( ev ){ if( Galaxy.frame && Galaxy.frame.active ){ - // Create frame with TabularChunkedView. - Galaxy.frame.add({ - title : "Data Viewer: " + self.model.get( 'name' ), - type : "other", - content : function( parent_elt ){ - require(['mvc/data'], function(DATA) { - var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) }); - $.when( new_dataset.fetch() ).then( function(){ - DATA.createTabularDatasetChunkedView({ - model: new_dataset, - parent_elt: parent_elt, - embedded: true, - height: '100%' - }); - }); - }); - } - }); + // Add dataset to frames. + Galaxy.frame.add_dataset(self.model.get('id')); ev.preventDefault(); } }; diff -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f -r 5808dd487257734f138833d5eed4d6a2d7e42f30 static/scripts/packed/galaxy.frame.js --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/ui/ui-frames"],function(b,c){var a=Backbone.View.extend({el_main:"body",active:false,button_active:null,button_load:null,initialize:function(e){var d=this;this.frames=new c.View({visible:false,});this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){if(d.frames.length()>0){return"You opened "+d.frames.length()+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){if(d.frames.visible){d.frames.hide()}else{d.frames.show()}},with_number:true});Galaxy.masthead.append(this.button_load);this.setElement(this.frames.$el);$(this.el_main).append(this.$el);this.frames.setOnChange(function(){d._refresh()});this._refresh()},add:function(e){if(e.target=="_blank"){window.open(e.content);return}if(e.target=="_top"||e.target=="_parent"||e.target=="_self"){window.location=e.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(e.target=="galaxy_main"||e.target=="center"){if(f.length===0){var d=e.content;if(d.indexOf("?")==-1){d+="?"}else{d+="&"}d+="use_panels=True";window.location=d}else{f.attr("src",e.content)}}else{window.location=e.content}return}this.frames.add(e)},_activate:function(){if(this.active){this.active=false;this.button_active.untoggle();this.frames.hide()}else{this.active=true;this.button_active.toggle()}},_refresh:function(){this.button_load.number(this.frames.length());if(this.frames.length()===0){this.button_load.hide()}else{this.button_load.show()}if(this.frames.visible){this.button_load.toggle()}else{this.button_load.untoggle()}}});return{GalaxyFrame:a}}); \ No newline at end of file +define(["galaxy.masthead","mvc/ui/ui-frames"],function(b,c){var a=Backbone.View.extend({el_main:"body",active:false,button_active:null,button_load:null,initialize:function(e){var d=this;this.frames=new c.View({visible:false,});this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){if(d.frames.length()>0){return"You opened "+d.frames.length()+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){if(d.frames.visible){d.frames.hide()}else{d.frames.show()}},with_number:true});Galaxy.masthead.append(this.button_load);this.setElement(this.frames.$el);$(this.el_main).append(this.$el);this.frames.setOnChange(function(){d._refresh()});this._refresh()},add_dataset:function(d){var e=this;require(["mvc/data"],function(f){var g=new f.Dataset({id:d});$.when(g.fetch()).then(function(){var h={title:g.get("name")},j=_.find(["tabular","interval"],function(k){return g.get("data_type").indexOf(k)!==-1});if(j){var i=new f.TabularDataset(g.toJSON());_.extend(h,{type:"other",content:function(k){f.createTabularDatasetChunkedView({model:i,parent_elt:k,embedded:true,height:"100%"})}})}else{_.extend(h,{type:"url",content:galaxy_config.root+"datasets/"+g.id+"/display/?preview=True"})}e.add(h)})})},add:function(e){if(e.target=="_blank"){window.open(e.content);return}if(e.target=="_top"||e.target=="_parent"||e.target=="_self"){window.location=e.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(e.target=="galaxy_main"||e.target=="center"){if(f.length===0){var d=e.content;if(d.indexOf("?")==-1){d+="?"}else{d+="&"}d+="use_panels=True";window.location=d}else{f.attr("src",e.content)}}else{window.location=e.content}return}this.frames.add(e)},_activate:function(){if(this.active){this.active=false;this.button_active.untoggle();this.frames.hide()}else{this.active=true;this.button_active.toggle()}},_refresh:function(){this.button_load.number(this.frames.length());if(this.frames.length()===0){this.button_load.hide()}else{this.button_load.show()}if(this.frames.visible){this.button_load.toggle()}else{this.button_load.untoggle()}}});return{GalaxyFrame:a}}); \ No newline at end of file diff -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f -r 5808dd487257734f138833d5eed4d6a2d7e42f30 static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.loading_chunk=false;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},expand_to_container:function(){if(this.$el.height()<this.scroll_elt.height()){this.attempt_to_fetch()}},attempt_to_fetch:function(n){var m=this;if(!this.loading_chunk&&this.scrolled_to_bottom()){this.loading_chunk=true;this.loading_indicator.show();$.when(m.model.get_next_chunk()).then(function(o){if(o){m._renderChunk(o);m.loading_chunk=false}m.loading_indicator.hide();m.expand_to_container()})}},render:function(){this.loading_indicator=$("<div/>").attr("id","loading_indicator");this.$el.append(this.loading_indicator);var p=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(p);var m=this.model.get_metadata("column_names"),q=$("<tr/>").css("background-color",this.header_color).appendTo(p);if(m){q.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(r){o._renderChunk(r)})}this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){if(o!==""){n.append(this._renderRow(o))}},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("file_ext")){return}this.file_ext=n.get("file_ext");if(this.file_ext=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.file_ext=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el);m.expand_to_container()}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){if(!this.get("metadata")){this._set_metadata()}this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.loading_chunk=false;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},expand_to_container:function(){if(this.$el.height()<this.scroll_elt.height()){this.attempt_to_fetch()}},attempt_to_fetch:function(n){var m=this;if(!this.loading_chunk&&this.scrolled_to_bottom()){this.loading_chunk=true;this.loading_indicator.show();$.when(m.model.get_next_chunk()).then(function(o){if(o){m._renderChunk(o);m.loading_chunk=false}m.loading_indicator.hide();m.expand_to_container()})}},render:function(){this.loading_indicator=$("<div/>").attr("id","loading_indicator");this.$el.append(this.loading_indicator);var p=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(p);var m=this.model.get_metadata("column_names"),q=$("<tr/>").css("background-color",this.header_color).appendTo(p);if(m){q.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(r){o._renderChunk(r)})}this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){if(o!==""){n.append(this._renderRow(o))}},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("file_ext")){return}this.file_ext=n.get("file_ext");if(this.file_ext=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.file_ext=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el);m.expand_to_container()}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file diff -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f -r 5808dd487257734f138833d5eed4d6a2d7e42f30 static/scripts/packed/mvc/dataset/dataset-li.js --- a/static/scripts/packed/mvc/dataset/dataset-li.js +++ b/static/scripts/packed/mvc/dataset/dataset-li.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(d,a,b,c){var f=d.ListItemView;var e=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);f.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this);this.model.on("change",function(h,g){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},_fetchModelDetails:function(){var g=this;if(g.model.inReadyState()&&!g.model.hasDetails()){return g.model.fetch({silent:true})}return jQuery.when()},remove:function(h,i){var g=this;h=h||this.fxSpeed;this.$el.fadeOut(h,function(){Backbone.View.prototype.remove.call(g);if(i){i.call(g)}})},render:function(g){return f.prototype.render.call(this,g)},_swapNewRender:function(g){f.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var i=this.model.get("state");if((i===a.NOT_VIEWABLE)||(i===a.DISCARDED)||(!this.model.get("accessible"))){return null}var h={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){h.disabled=true;h.title=c("Cannot display datasets removed from disk")}else{if(i===a.UPLOAD){h.disabled=true;h.title=c("This dataset must finish uploading before it can be viewed")}else{if(i===a.NEW){h.disabled=true;h.title=c("This dataset is not yet viewable")}else{h.title=c("View data");h.href=this.model.urls.display;var g=this;h.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+g.model.get("name"),type:"other",content:function(k){require(["mvc/data"],function(l){var m=new l.TabularDataset({id:g.model.get("id")});$.when(m.fetch()).then(function(){l.createTabularDatasetChunkedView({model:m,parent_elt:k,embedded:true,height:"100%"})})})}});j.preventDefault()}}}}}h.faIcon="fa-eye";return faIconButton(h)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var g=f.prototype._renderDetails.call(this);g.find(".actions .left").empty().append(this._renderSecondaryActions());g.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());g.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(g);return g},_renderSummary:function(){var g=this.model.toJSON(),h=this.templates.summaries[g.state];h=h||this.templates.summaries.unknown;return h(g,this)},_renderDetailMessages:function(){var g=this,i=$('<div class="detail-messages"></div>'),h=g.model.toJSON();_.each(g.templates.detailMessages,function(j){i.append($(j(h,g)))});return i},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var g=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+g.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(h){return['<li><a href="',g.meta_download+h.file_type,'">',c("Download")," ",h.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(g){this.trigger("display",this,g)},"click .params-btn":function(g){this.trigger("params",this,g)},"click .download-btn":function(g){this.trigger("download",this,g)}}),toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+g+")"}});e.prototype.templates=(function(){var i=_.extend({},f.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var j=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var h=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var k={};k[a.OK]=k[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");k[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");k[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");k[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");k[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");k[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");k[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");k[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");k[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");k[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");k[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");k.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var l={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var g=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:i,details:j,noAccess:h,summaries:k,detailMessages:l,displayApplications:g})}());return{DatasetListItemView:e}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(d,a,b,c){var f=d.ListItemView;var e=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);f.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this);this.model.on("change",function(h,g){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},_fetchModelDetails:function(){var g=this;if(g.model.inReadyState()&&!g.model.hasDetails()){return g.model.fetch({silent:true})}return jQuery.when()},remove:function(h,i){var g=this;h=h||this.fxSpeed;this.$el.fadeOut(h,function(){Backbone.View.prototype.remove.call(g);if(i){i.call(g)}})},render:function(g){return f.prototype.render.call(this,g)},_swapNewRender:function(g){f.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var i=this.model.get("state");if((i===a.NOT_VIEWABLE)||(i===a.DISCARDED)||(!this.model.get("accessible"))){return null}var h={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){h.disabled=true;h.title=c("Cannot display datasets removed from disk")}else{if(i===a.UPLOAD){h.disabled=true;h.title=c("This dataset must finish uploading before it can be viewed")}else{if(i===a.NEW){h.disabled=true;h.title=c("This dataset is not yet viewable")}else{h.title=c("View data");h.href=this.model.urls.display;var g=this;h.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add_dataset(g.model.get("id"));j.preventDefault()}}}}}h.faIcon="fa-eye";return faIconButton(h)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var g=f.prototype._renderDetails.call(this);g.find(".actions .left").empty().append(this._renderSecondaryActions());g.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());g.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(g);return g},_renderSummary:function(){var g=this.model.toJSON(),h=this.templates.summaries[g.state];h=h||this.templates.summaries.unknown;return h(g,this)},_renderDetailMessages:function(){var g=this,i=$('<div class="detail-messages"></div>'),h=g.model.toJSON();_.each(g.templates.detailMessages,function(j){i.append($(j(h,g)))});return i},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var g=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+g.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(h){return['<li><a href="',g.meta_download+h.file_type,'">',c("Download")," ",h.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(g){this.trigger("display",this,g)},"click .params-btn":function(g){this.trigger("params",this,g)},"click .download-btn":function(g){this.trigger("download",this,g)}}),toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+g+")"}});e.prototype.templates=(function(){var i=_.extend({},f.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var j=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var h=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var k={};k[a.OK]=k[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");k[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");k[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");k[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");k[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");k[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");k[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");k[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");k[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");k[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");k[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");k.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var l={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var g=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:i,details:j,noAccess:h,summaries:k,detailMessages:l,displayApplications:g})}());return{DatasetListItemView:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] b9e31d: Update Pulsar on Test.
by GitHub 24 Sep '14

24 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b9e31dd35aa11818c894471a970acda41564c33c https://github.com/galaxyproject/usegalaxy-playbook/commit/b9e31dd35aa11818… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Pulsar on Test.

1 0

[galaxyproject/usegalaxy-playbook] afe4f4: *Actually* add Stampede to cuff* (!cuffcompare) on...
by GitHub 24 Sep '14

24 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: afe4f48927830c7a29e9cbdfc9b1b742933ed630 https://github.com/galaxyproject/usegalaxy-playbook/commit/afe4f48927830c7a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- *Actually* add Stampede to cuff* (!cuffcompare) on Main.

1 0

commit/galaxy-central: jgoecks: Fix dataset loading in Scratchbook: if dataset is tabular, load dynamically without iframe; otherwise load into iframe.
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/83aaac537783/ Changeset: 83aaac537783 Branch: next-stable User: jgoecks Date: 2014-09-24 17:26:55+00:00 Summary: Fix dataset loading in Scratchbook: if dataset is tabular, load dynamically without iframe; otherwise load into iframe. Affected #: 6 files diff -r 780b4d933899b6ccbc025568caaa4860e65faaba -r 83aaac537783198aa18da52e0bccc31018ef968a static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -73,8 +73,59 @@ }); this._refresh(); }, + + /** + * Add a dataset to the frames. + */ + add_dataset: function(dataset_id) { + var self = this; + require(['mvc/data'], function(DATA) { + var dataset = new DATA.Dataset({ id: dataset_id }); + $.when( dataset.fetch() ).then( function() { + // Construct frame config based on dataset's type. + var frame_config = { + title: dataset.get('name') + }, + // HACK: For now, assume 'tabular' and 'interval' are the only + // modules that contain tabular files. This needs to be replaced + // will a is_datatype() function. + is_tabular = _.find(['tabular', 'interval'], function(data_type) { + return dataset.get('data_type').indexOf(data_type) !== -1; + }); + + // Use tabular chunked display if dataset is tabular; otherwise load via URL. + if (is_tabular) { + var tabular_dataset = new DATA.TabularDataset(dataset.toJSON()); + _.extend(frame_config, { + type: 'other', + content: function( parent_elt ) { + DATA.createTabularDatasetChunkedView({ + model: tabular_dataset, + parent_elt: parent_elt, + embedded: true, + height: '100%' + }); + } + }); + } + else { + _.extend(frame_config, { + type: 'url', + content: galaxy_config.root + 'datasets/' + + dataset.id + '/display/?preview=True' + }); + } + + self.add(frame_config); + + }); + }); + + }, - // adds and displays a new frame/window + /** + * Add and display a new frame/window based on options. + */ add: function(options) { // open new tab diff -r 780b4d933899b6ccbc025568caaa4860e65faaba -r 83aaac537783198aa18da52e0bccc31018ef968a static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -20,7 +20,11 @@ }, initialize: function() { - this._set_metadata(); + // Metadata can be passed in as a model or a set of attributes; if it's + // already a model, there's no need to set metadata. + if (!this.get('metadata')) { + this._set_metadata(); + } // Update metadata on change. this.on('change', this._set_metadata, this); diff -r 780b4d933899b6ccbc025568caaa4860e65faaba -r 83aaac537783198aa18da52e0bccc31018ef968a static/scripts/mvc/dataset/dataset-li.js --- a/static/scripts/mvc/dataset/dataset-li.js +++ b/static/scripts/mvc/dataset/dataset-li.js @@ -161,24 +161,8 @@ var self = this; displayBtnData.onclick = function( ev ){ if( Galaxy.frame && Galaxy.frame.active ){ - // Create frame with TabularChunkedView. - Galaxy.frame.add({ - title : "Data Viewer: " + self.model.get( 'name' ), - type : "other", - content : function( parent_elt ){ - require(['mvc/data'], function(DATA) { - var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) }); - $.when( new_dataset.fetch() ).then( function(){ - DATA.createTabularDatasetChunkedView({ - model: new_dataset, - parent_elt: parent_elt, - embedded: true, - height: '100%' - }); - }); - }); - } - }); + // Add dataset to frames. + Galaxy.frame.add_dataset(self.model.get('id')); ev.preventDefault(); } }; diff -r 780b4d933899b6ccbc025568caaa4860e65faaba -r 83aaac537783198aa18da52e0bccc31018ef968a static/scripts/packed/galaxy.frame.js --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/ui/ui-frames"],function(b,c){var a=Backbone.View.extend({el_main:"body",active:false,button_active:null,button_load:null,initialize:function(e){var d=this;this.frames=new c.View({visible:false,});this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){if(d.frames.length()>0){return"You opened "+d.frames.length()+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){if(d.frames.visible){d.frames.hide()}else{d.frames.show()}},with_number:true});Galaxy.masthead.append(this.button_load);this.setElement(this.frames.$el);$(this.el_main).append(this.$el);this.frames.setOnChange(function(){d._refresh()});this._refresh()},add:function(e){if(e.target=="_blank"){window.open(e.content);return}if(e.target=="_top"||e.target=="_parent"||e.target=="_self"){window.location=e.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(e.target=="galaxy_main"||e.target=="center"){if(f.length===0){var d=e.content;if(d.indexOf("?")==-1){d+="?"}else{d+="&"}d+="use_panels=True";window.location=d}else{f.attr("src",e.content)}}else{window.location=e.content}return}this.frames.add(e)},_activate:function(){if(this.active){this.active=false;this.button_active.untoggle();this.frames.hide()}else{this.active=true;this.button_active.toggle()}},_refresh:function(){this.button_load.number(this.frames.length());if(this.frames.length()===0){this.button_load.hide()}else{this.button_load.show()}if(this.frames.visible){this.button_load.toggle()}else{this.button_load.untoggle()}}});return{GalaxyFrame:a}}); \ No newline at end of file +define(["galaxy.masthead","mvc/ui/ui-frames"],function(b,c){var a=Backbone.View.extend({el_main:"body",active:false,button_active:null,button_load:null,initialize:function(e){var d=this;this.frames=new c.View({visible:false,});this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(){d._activate()},onunload:function(){if(d.frames.length()>0){return"You opened "+d.frames.length()+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){if(d.frames.visible){d.frames.hide()}else{d.frames.show()}},with_number:true});Galaxy.masthead.append(this.button_load);this.setElement(this.frames.$el);$(this.el_main).append(this.$el);this.frames.setOnChange(function(){d._refresh()});this._refresh()},add_dataset:function(d){var e=this;require(["mvc/data"],function(f){var g=new f.Dataset({id:d});$.when(g.fetch()).then(function(){var h={title:g.get("name")},j=_.find(["tabular","interval"],function(k){return g.get("data_type").indexOf(k)!==-1});if(j){var i=new f.TabularDataset(g.toJSON());_.extend(h,{type:"other",content:function(k){f.createTabularDatasetChunkedView({model:i,parent_elt:k,embedded:true,height:"100%"})}})}else{_.extend(h,{type:"url",content:galaxy_config.root+"datasets/"+g.id+"/display/?preview=True"})}e.add(h)})})},add:function(e){if(e.target=="_blank"){window.open(e.content);return}if(e.target=="_top"||e.target=="_parent"||e.target=="_self"){window.location=e.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(e.target=="galaxy_main"||e.target=="center"){if(f.length===0){var d=e.content;if(d.indexOf("?")==-1){d+="?"}else{d+="&"}d+="use_panels=True";window.location=d}else{f.attr("src",e.content)}}else{window.location=e.content}return}this.frames.add(e)},_activate:function(){if(this.active){this.active=false;this.button_active.untoggle();this.frames.hide()}else{this.active=true;this.button_active.toggle()}},_refresh:function(){this.button_load.number(this.frames.length());if(this.frames.length()===0){this.button_load.hide()}else{this.button_load.show()}if(this.frames.visible){this.button_load.toggle()}else{this.button_load.untoggle()}}});return{GalaxyFrame:a}}); \ No newline at end of file diff -r 780b4d933899b6ccbc025568caaa4860e65faaba -r 83aaac537783198aa18da52e0bccc31018ef968a static/scripts/packed/mvc/data.js --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.loading_chunk=false;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},expand_to_container:function(){if(this.$el.height()<this.scroll_elt.height()){this.attempt_to_fetch()}},attempt_to_fetch:function(n){var m=this;if(!this.loading_chunk&&this.scrolled_to_bottom()){this.loading_chunk=true;this.loading_indicator.show();$.when(m.model.get_next_chunk()).then(function(o){if(o){m._renderChunk(o);m.loading_chunk=false}m.loading_indicator.hide();m.expand_to_container()})}},render:function(){this.loading_indicator=$("<div/>").attr("id","loading_indicator");this.$el.append(this.loading_indicator);var p=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(p);var m=this.model.get_metadata("column_names"),q=$("<tr/>").css("background-color",this.header_color).appendTo(p);if(m){q.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(r){o._renderChunk(r)})}this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){if(o!==""){n.append(this._renderRow(o))}},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("file_ext")){return}this.file_ext=n.get("file_ext");if(this.file_ext=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.file_ext=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el);m.expand_to_container()}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file +define(["mvc/ui/ui-modal","mvc/ui/ui-frames"],function(j,i){var g=Backbone.Model.extend({});var b=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){if(!this.get("metadata")){this._set_metadata()}this.on("change",this._set_metadata,this)},_set_metadata:function(){var m=new g();_.each(_.keys(this.attributes),function(n){if(n.indexOf("metadata_")===0){var o=n.split("metadata_")[1];m.set(o,this.attributes[n]);delete this.attributes[n]}},this);this.set("metadata",m,{silent:true})},get_metadata:function(m){return this.attributes.metadata.get(m)},urlRoot:galaxy_config.root+"api/datasets"});var h=b.extend({defaults:_.extend({},b.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(m){b.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0);this.attributes.chunk_url=galaxy_config.root+"dataset/display?dataset_id="+this.id;this.attributes.url_viz=galaxy_config.root+"visualization"},get_next_chunk:function(){if(this.attributes.at_eof){return null}var m=this,n=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:m.attributes.chunk_index++}).success(function(o){var p;if(o.ck_data!==""){p=o}else{m.attributes.at_eof=true;p=null}n.resolve(p)});return n}});var e=Backbone.Collection.extend({model:b});var a=Backbone.View.extend({initialize:function(m){this.row_count=0;this.loading_chunk=false;this.header_color="#AAA";this.dark_row_color="#DDD";new d({model:m.model,$el:this.$el})},expand_to_container:function(){if(this.$el.height()<this.scroll_elt.height()){this.attempt_to_fetch()}},attempt_to_fetch:function(n){var m=this;if(!this.loading_chunk&&this.scrolled_to_bottom()){this.loading_chunk=true;this.loading_indicator.show();$.when(m.model.get_next_chunk()).then(function(o){if(o){m._renderChunk(o);m.loading_chunk=false}m.loading_indicator.hide();m.expand_to_container()})}},render:function(){this.loading_indicator=$("<div/>").attr("id","loading_indicator");this.$el.append(this.loading_indicator);var p=$("<table/>").attr({id:"content_table",cellpadding:0});this.$el.append(p);var m=this.model.get_metadata("column_names"),q=$("<tr/>").css("background-color",this.header_color).appendTo(p);if(m){q.append("<th>"+m.join("</th><th>")+"</th>")}var o=this,n=this.model.get("first_data_chunk");if(n){this._renderChunk(n)}else{$.when(o.model.get_next_chunk()).then(function(r){o._renderChunk(r)})}this.scroll_elt.scroll(function(){o.attempt_to_fetch()})},scrolled_to_bottom:function(){return false},_renderCell:function(p,m,q){var n=$("<td>").text(p);var o=this.model.get_metadata("column_types");if(q!==undefined){n.attr("colspan",q).addClass("stringalign")}else{if(o){if(m<o.length){if(o[m]==="str"||o[m]==="list"){n.addClass("stringalign")}}}}return n},_renderRow:function(m){var n=m.split("\t"),p=$("<tr>"),o=this.model.get_metadata("columns");if(this.row_count%2!==0){p.css("background-color",this.dark_row_color)}if(n.length===o){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this)}else{if(n.length>o){_.each(n.slice(0,o-1),function(r,q){p.append(this._renderCell(r,q))},this);p.append(this._renderCell(n.slice(o-1).join("\t"),o-1))}else{if(o>5&&n.length===o-1){_.each(n,function(r,q){p.append(this._renderCell(r,q))},this);p.append($("<td>"))}else{p.append(this._renderCell(m,0,o))}}}this.row_count++;return p},_renderChunk:function(m){var n=this.$el.find("table");_.each(m.ck_data.split("\n"),function(o,p){if(o!==""){n.append(this._renderRow(o))}},this)}});var f=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);scroll_elt=_.find(this.$el.parents(),function(n){return $(n).css("overflow")==="auto"});if(!scroll_elt){scroll_elt=window}this.scroll_elt=$(scroll_elt)},scrolled_to_bottom:function(){return(this.$el.height()-this.scroll_elt.scrollTop()-this.scroll_elt.height()<=0)}});var l=a.extend({initialize:function(m){a.prototype.initialize.call(this,m);this.scroll_elt=this.$el.css({position:"relative",overflow:"scroll",height:this.options.height||"500px"})},scrolled_to_bottom:function(){return this.$el.scrollTop()+this.$el.innerHeight()>=this.el.scrollHeight}});var d=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,file_ext:null,initialize:function(o){var r=parent.Galaxy;if(r&&r.modal){this.modal=r.modal}if(r&&r.frame){this.frame=r.frame}if(!this.modal||!this.frame){return}var n=o.model;var q=n.get("metadata");if(!n.get("file_ext")){return}this.file_ext=n.get("file_ext");if(this.file_ext=="bed"){if(q.get("chromCol")&&q.get("startCol")&&q.get("endCol")){this.col.chrom=q.get("chromCol")-1;this.col.start=q.get("startCol")-1;this.col.end=q.get("endCol")-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.");return}}if(this.file_ext=="vcf"){function p(t,u){for(var s=0;s<u.length;s++){if(u[s].match(t)){return s}}return -1}this.col.chrom=p("Chrom",q.get("column_names"));this.col.start=p("Pos",q.get("column_names"));this.col.end=null;if(this.col.chrom==-1||this.col.start==-1){console.log("TabularButtonTrackster : VCF-file metadata incomplete.");return}}if(this.col.chrom===undefined){return}if(n.id){this.dataset_id=n.id}else{console.log("TabularButtonTrackster : Dataset identification is missing.");return}if(n.get("url_viz")){this.url_viz=n.get("url_viz")}else{console.log("TabularButtonTrackster : Url for visualization controller is missing.");return}if(n.get("genome_build")){this.genome_build=n.get("genome_build")}var m=new IconButtonView({model:new IconButton({title:"Visualize",icon_class:"chart_curve",id:"btn_viz"})});this.setElement(o.$el);this.$el.append(m.render().$el);this.hide()},events:{"mouseover tr":"show",mouseleave:"hide"},show:function(r){function q(w){return !isNaN(parseFloat(w))&&isFinite(w)}if(this.col.chrom===null){return}var v=$(r.target).parent();var s=v.children().eq(this.col.chrom).html();var m=v.children().eq(this.col.start).html();var o=this.col.end?v.children().eq(this.col.end).html():m;if(!s.match("^#")&&s!==""&&q(m)){var u={dataset_id:this.dataset_id,gene_region:s+":"+m+"-"+o};var p=v.offset();var n=p.left-10;var t=p.top-$(window).scrollTop()+3;$("#btn_viz").css({position:"fixed",top:t+"px",left:n+"px"});$("#btn_viz").off("click");$("#btn_viz").click(this.create_trackster_action(this.url_viz,u,this.genome_build));$("#btn_viz").show()}else{$("#btn_viz").hide()}},hide:function(){this.$el.find("#btn_viz").hide()},create_trackster_action:function(m,p,o){var n=this;return function(){var q={};if(o){q["f-dbkey"]=o}$.ajax({url:m+"/list_tracks?"+$.param(q),dataType:"html",error:function(){n.modal.show({title:"Something went wrong!",body:"Unfortunately we could not add this dataset to the track browser. Please try again or contact us.",buttons:{Cancel:function(){n.modal.hide()}}})},success:function(r){n.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){n.modal.hide()},"View in saved visualization":function(){n.modal.show({title:"Add Data to Saved Visualization",body:r,buttons:{Cancel:function(){n.modal.hide()},"Add to visualization":function(){n.modal.hide();n.modal.$el.find("input[name=id]:checked").each(function(){var s=$(this).val();p.id=s;n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})})}}})},"View in new visualization":function(){n.modal.hide();n.frame.add({title:"Trackster",type:"url",content:m+"/trackster?"+$.param(p)})}}})}});return false}}});var k=function(p,n,q,m){var o=new n({model:new p(q)});o.render();if(m){m.append(o.$el)}return o};var c=function(o){if(!o.model){o.model=new h(o.dataset_config)}var n=o.parent_elt;var p=o.embedded;delete o.embedded;delete o.parent_elt;delete o.dataset_config;var m=(p?new l(o):new f(o));m.render();if(n){n.append(m.$el);m.expand_to_container()}return m};return{Dataset:b,TabularDataset:h,DatasetCollection:e,TabularDatasetChunkedView:a,createTabularDatasetChunkedView:c}}); \ No newline at end of file diff -r 780b4d933899b6ccbc025568caaa4860e65faaba -r 83aaac537783198aa18da52e0bccc31018ef968a static/scripts/packed/mvc/dataset/dataset-li.js --- a/static/scripts/packed/mvc/dataset/dataset-li.js +++ b/static/scripts/packed/mvc/dataset/dataset-li.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(d,a,b,c){var f=d.ListItemView;var e=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);f.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this);this.model.on("change",function(h,g){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},_fetchModelDetails:function(){var g=this;if(g.model.inReadyState()&&!g.model.hasDetails()){return g.model.fetch({silent:true})}return jQuery.when()},remove:function(h,i){var g=this;h=h||this.fxSpeed;this.$el.fadeOut(h,function(){Backbone.View.prototype.remove.call(g);if(i){i.call(g)}})},render:function(g){return f.prototype.render.call(this,g)},_swapNewRender:function(g){f.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var i=this.model.get("state");if((i===a.NOT_VIEWABLE)||(i===a.DISCARDED)||(!this.model.get("accessible"))){return null}var h={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){h.disabled=true;h.title=c("Cannot display datasets removed from disk")}else{if(i===a.UPLOAD){h.disabled=true;h.title=c("This dataset must finish uploading before it can be viewed")}else{if(i===a.NEW){h.disabled=true;h.title=c("This dataset is not yet viewable")}else{h.title=c("View data");h.href=this.model.urls.display;var g=this;h.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+g.model.get("name"),type:"other",content:function(k){require(["mvc/data"],function(l){var m=new l.TabularDataset({id:g.model.get("id")});$.when(m.fetch()).then(function(){l.createTabularDatasetChunkedView({model:m,parent_elt:k,embedded:true,height:"100%"})})})}});j.preventDefault()}}}}}h.faIcon="fa-eye";return faIconButton(h)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var g=f.prototype._renderDetails.call(this);g.find(".actions .left").empty().append(this._renderSecondaryActions());g.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());g.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(g);return g},_renderSummary:function(){var g=this.model.toJSON(),h=this.templates.summaries[g.state];h=h||this.templates.summaries.unknown;return h(g,this)},_renderDetailMessages:function(){var g=this,i=$('<div class="detail-messages"></div>'),h=g.model.toJSON();_.each(g.templates.detailMessages,function(j){i.append($(j(h,g)))});return i},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var g=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+g.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(h){return['<li><a href="',g.meta_download+h.file_type,'">',c("Download")," ",h.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(g){this.trigger("display",this,g)},"click .params-btn":function(g){this.trigger("params",this,g)},"click .download-btn":function(g){this.trigger("download",this,g)}}),toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+g+")"}});e.prototype.templates=(function(){var i=_.extend({},f.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var j=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var h=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var k={};k[a.OK]=k[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");k[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");k[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");k[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");k[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");k[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");k[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");k[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");k[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");k[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");k[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");k.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var l={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var g=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:i,details:j,noAccess:h,summaries:k,detailMessages:l,displayApplications:g})}());return{DatasetListItemView:e}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/dataset/states","mvc/base-mvc","utils/localization"],function(d,a,b,c){var f=d.ListItemView;var e=f.extend({className:f.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(g){if(g.logger){this.logger=this.model.logger=g.logger}this.log(this+".initialize:",g);f.prototype.initialize.call(this,g);this.linkTarget=g.linkTarget||"_blank";this._setUpListeners()},_setUpListeners:function(){f.prototype._setUpListeners.call(this);this.model.on("change",function(h,g){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},_fetchModelDetails:function(){var g=this;if(g.model.inReadyState()&&!g.model.hasDetails()){return g.model.fetch({silent:true})}return jQuery.when()},remove:function(h,i){var g=this;h=h||this.fxSpeed;this.$el.fadeOut(h,function(){Backbone.View.prototype.remove.call(g);if(i){i.call(g)}})},render:function(g){return f.prototype.render.call(this,g)},_swapNewRender:function(g){f.prototype._swapNewRender.call(this,g);if(this.model.has("state")){this.$el.addClass("state-"+this.model.get("state"))}return this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var i=this.model.get("state");if((i===a.NOT_VIEWABLE)||(i===a.DISCARDED)||(!this.model.get("accessible"))){return null}var h={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged")){h.disabled=true;h.title=c("Cannot display datasets removed from disk")}else{if(i===a.UPLOAD){h.disabled=true;h.title=c("This dataset must finish uploading before it can be viewed")}else{if(i===a.NEW){h.disabled=true;h.title=c("This dataset is not yet viewable")}else{h.title=c("View data");h.href=this.model.urls.display;var g=this;h.onclick=function(j){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add_dataset(g.model.get("id"));j.preventDefault()}}}}}h.faIcon="fa-eye";return faIconButton(h)},_renderDetails:function(){if(this.model.get("state")===a.NOT_VIEWABLE){return $(this.templates.noAccess(this.model.toJSON(),this))}var g=f.prototype._renderDetails.call(this);g.find(".actions .left").empty().append(this._renderSecondaryActions());g.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages());g.find(".display-applications").html(this._renderDisplayApplications());this._setUpBehaviors(g);return g},_renderSummary:function(){var g=this.model.toJSON(),h=this.templates.summaries[g.state];h=h||this.templates.summaries.unknown;return h(g,this)},_renderDetailMessages:function(){var g=this,i=$('<div class="detail-messages"></div>'),h=g.model.toJSON();_.each(g.templates.detailMessages,function(j){i.append($(j(h,g)))});return i},_renderDisplayApplications:function(){if(this.model.isDeletedOrPurged()){return""}return[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){this.debug("_renderSecondaryActions");switch(this.model.get("state")){case a.NOT_VIEWABLE:return[];case a.OK:case a.FAILED_METADATA:case a.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return faIconButton({title:c("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}if(!_.isEmpty(this.model.get("meta_files"))){return this._renderMetaFileDownloadButton()}return $(['<a class="download-btn icon-btn" href="',this.model.urls.download,'" title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))},_renderMetaFileDownloadButton:function(){var g=this.model.urls;return $(['<div class="metafile-dropdown dropdown">','<a class="download-btn icon-btn" href="javascript:void(0)" data-toggle="dropdown"',' title="'+c("Download")+'">','<span class="fa fa-floppy-o"></span>',"</a>",'<ul class="dropdown-menu" role="menu" aria-labelledby="dLabel">','<li><a href="'+g.download+'">',c("Download dataset"),"</a></li>",_.map(this.model.get("meta_files"),function(h){return['<li><a href="',g.meta_download+h.file_type,'">',c("Download")," ",h.file_type,"</a></li>"].join("")}).join("\n"),"</ul>","</div>"].join("\n"))},events:_.extend(_.clone(f.prototype.events),{"click .display-btn":function(g){this.trigger("display",this,g)},"click .params-btn":function(g){this.trigger("params",this,g)},"click .download-btn":function(g){this.trigger("download",this,g)}}),toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"DatasetListItemView("+g+")"}});e.prototype.templates=(function(){var i=_.extend({},f.prototype.templates.warnings,{failed_metadata:b.wrapTemplate(['<% if( model.state === "failed_metadata" ){ %>','<div class="warningmessagesmall">',c("An error occurred setting the metadata for this dataset"),"</div>","<% } %>"]),error:b.wrapTemplate(["<% if( model.error ){ %>",'<div class="errormessagesmall">',c("There was an error getting the data for this dataset"),": <%- model.error %>","</div>","<% } %>"]),purged:b.wrapTemplate(["<% if( model.purged ){ %>",'<div class="purged-msg warningmessagesmall">',c("This dataset has been deleted and removed from disk"),"</div>","<% } %>"]),deleted:b.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'<div class="deleted-msg warningmessagesmall">',c("This dataset has been deleted"),"</div>","<% } %>"])});var j=b.wrapTemplate(['<div class="details">','<div class="summary"></div>','<div class="actions clear">','<div class="left"></div>','<div class="right"></div>',"</div>","<% if( !dataset.deleted && !dataset.purged ){ %>",'<div class="tags-display"></div>','<div class="annotation-display"></div>','<div class="display-applications"></div>',"<% if( dataset.peek ){ %>",'<pre class="dataset-peek"><%= dataset.peek %></pre>',"<% } %>","<% } %>","</div>"],"dataset");var h=b.wrapTemplate(['<div class="details">','<div class="summary">',c("You do not have permission to view this dataset"),"</div>","</div>"],"dataset");var k={};k[a.OK]=k[a.FAILED_METADATA]=b.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'<div class="blurb">','<span class="value"><%- dataset.misc_blurb %></span>',"</div>","<% } %>","<% if( dataset.file_ext ){ %>",'<div class="datatype">','<label class="prompt">',c("format"),"</label>",'<span class="value"><%- dataset.file_ext %></span>',"</div>","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'<div class="dbkey">','<label class="prompt">',c("database"),"</label>",'<span class="value">',"<%- dataset.metadata_dbkey %>","</span>","</div>","<% } %>","<% if( dataset.misc_info ){ %>",'<div class="info">','<span class="value"><%- dataset.misc_info %></span>',"</div>","<% } %>"],"dataset");k[a.NEW]=b.wrapTemplate(["<div>",c("This is a new dataset and not all of its data are available yet"),"</div>"],"dataset");k[a.NOT_VIEWABLE]=b.wrapTemplate(["<div>",c("You do not have permission to view this dataset"),"</div>"],"dataset");k[a.DISCARDED]=b.wrapTemplate(["<div>",c("The job creating this dataset was cancelled before completion"),"</div>"],"dataset");k[a.QUEUED]=b.wrapTemplate(["<div>",c("This job is waiting to run"),"</div>"],"dataset");k[a.RUNNING]=b.wrapTemplate(["<div>",c("This job is currently running"),"</div>"],"dataset");k[a.UPLOAD]=b.wrapTemplate(["<div>",c("This dataset is currently uploading"),"</div>"],"dataset");k[a.SETTING_METADATA]=b.wrapTemplate(["<div>",c("Metadata is being auto-detected"),"</div>"],"dataset");k[a.PAUSED]=b.wrapTemplate(["<div>",c('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"</div>"],"dataset");k[a.ERROR]=b.wrapTemplate(["<% if( !dataset.purged ){ %>","<div><%- dataset.misc_blurb %></div>","<% } %>",'<span class="help-text">',c("An error occurred with this dataset"),":</span>",'<div class="job-error-text"><%- dataset.misc_info %></div>'],"dataset");k[a.EMPTY]=b.wrapTemplate(["<div>",c("No data"),": <i><%- dataset.misc_blurb %></i></div>"],"dataset");k.unknown=b.wrapTemplate(['<div>Error: unknown dataset state: "<%- dataset.state %>"</div>'],"dataset");var l={resubmitted:b.wrapTemplate(["<% if( model.resubmitted ){ %>",'<div class="resubmitted-msg infomessagesmall">',c("The job creating this dataset has been resubmitted"),"</div>","<% } %>"])};var g=b.wrapTemplate(["<% _.each( apps, function( app ){ %>",'<div class="display-application">','<span class="display-application-location"><%- app.label %></span> ','<span class="display-application-links">',"<% _.each( app.links, function( link ){ %>",'<a target="<%= link.target %>" href="<%= link.href %>">',"<% print( _l( link.text ) ); %>","</a> ","<% }); %>","</span>","</div>","<% }); %>"],"apps");return _.extend({},f.prototype.templates,{warnings:i,details:j,noAccess:h,summaries:k,detailMessages:l,displayApplications:g})}());return{DatasetListItemView:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] 1293cf: Add Stampede to cuff* (!cuffcompare) on Main.
by GitHub 24 Sep '14

24 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1293cf92388a95305770baf3681f5623d6eb431f https://github.com/galaxyproject/usegalaxy-playbook/commit/1293cf92388a9530… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Add Stampede to cuff* (!cuffcompare) on Main.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/780b4d933899/ Changeset: 780b4d933899 Branch: next-stable User: carlfeberhard Date: 2014-09-24 16:14:13+00:00 Summary: Fix history/view to allow scolling when use_panels=True Affected #: 1 file diff -r 01f7ec31bc8161e7731c25df374495eac6425ba8 -r 780b4d933899b6ccbc025568caaa4860e65faaba templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -134,8 +134,8 @@ }); $( '#switch' ).click( function( ev ){ - ##HACK:ity hack hack - ##TODO: remove when out of iframe + //##HACK:ity hack hack + //##TODO: remove when out of iframe var hpanel = Galaxy.currHistoryPanel || ( top.Galaxy && top.Galaxy.currHistoryPanel )? top.Galaxy.currHistoryPanel : null; if( hpanel ){ @@ -163,9 +163,12 @@ }); } - var userIsOwner = ${'true' if user_is_owner else 'false'}, + // use_panels effects where the the center_panel() is rendered: + // w/o it renders to the body, w/ it renders to #center - we need to adjust a few things for scrolling to work + var hasMasthead = ${ 'true' if use_panels else 'false' }, + userIsOwner = ${'true' if user_is_owner else 'false'}, historyJSON = ${h.dumps( history )}, - hdaJSON = ${h.dumps( hdas )}; + hdaJSON = ${h.dumps( hdas )}, panelToUse = ( userIsOwner )? //TODO: change class names ({ location: 'mvc/history/history-panel-edit', className: 'HistoryPanelEdit' }): @@ -176,6 +179,9 @@ })([ 'mvc/user/user-model', panelToUse.location, 'utils/localization' ], function( user, panelMod, _l ){ $(function(){ setUpBehaviors(); + if( hasMasthead ){ + $( '#center' ).css( 'overflow', 'auto' ); + } var panelClass = panelMod[ panelToUse.className ], // history module is already in the dpn chain from the panel. We can re-scope it here. @@ -187,6 +193,7 @@ show_hidden : ${show_hidden_json}, purgeAllowed : Galaxy.config.allow_user_dataset_purge, el : $( "#history-" + historyJSON.id ), + $scrollContainer: hasMasthead? function(){ return this.$el.parent(); } : undefined, model : history }).render(); https://bitbucket.org/galaxy/galaxy-central/commits/9ebe2f6ecb52/ Changeset: 9ebe2f6ecb52 User: carlfeberhard Date: 2014-09-24 16:14:33+00:00 Summary: Merge default Affected #: 15 files diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -9f495158c5ba45fcf61fc37d82aa8545eaba0bd5 latest_2014.08.11 +9f15bf53a11b8a91301381d836271a0ac3b23e71 latest_2014.08.11 diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f client/galaxy/scripts/galaxy.base.js --- a/client/galaxy/scripts/galaxy.base.js +++ b/client/galaxy/scripts/galaxy.base.js @@ -236,9 +236,10 @@ $.fn.refresh_select2 = function() { var select_elt = $(this); - var options = { width: "resolve", + var options = { placeholder:'Click to select', closeOnSelect: !select_elt.is("[MULTIPLE]"), - dropdownAutoWidth : true + dropdownAutoWidth : true, + containerCssClass: 'select2-minwidth' }; return select_elt.select2( options ); } diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f client/galaxy/scripts/mvc/library/library-dataset-view.js --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -117,7 +117,7 @@ downloadDataset: function(){ var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : this.id}; + var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -275,7 +275,7 @@ } } ); var url = '/api/libraries/datasets/download/' + format; - var data = { 'ldda_ids' : dataset_ids }; + var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml @@ -3,7 +3,10 @@ <requirements><requirement type="package">ucsc_tools</requirement></requirements> - <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command> + <command> + grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output + 2>&1 || echo "Error running wiggle to bigwig converter." >&2 + </command><inputs><page><param format="wig" name="input" type="data" label="Choose wiggle"/> diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -518,31 +518,30 @@ :param format: string representing requested archive format :type format: string - :param lddas[]: an array of encoded ids - :type lddas[]: an array + :param ld_ids[]: an array of encoded ids + :type ld_ids[]: an array :rtype: file :returns: either archive with the requested datasets packed inside or a single uncompressed dataset :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound """ - lddas = [] - datasets_to_download = kwd.get( 'ldda_ids%5B%5D', None ) + library_datasets = [] + datasets_to_download = kwd.get( 'ld_ids%5B%5D', None ) if datasets_to_download is None: - datasets_to_download = kwd.get( 'ldda_ids', None ) - + datasets_to_download = kwd.get( 'ld_ids', None ) if ( datasets_to_download is not None ): datasets_to_download = util.listify( datasets_to_download ) for dataset_id in datasets_to_download: try: - ldda = self.get_hda_or_ldda( trans, hda_ldda='ldda', dataset_id=dataset_id ) - lddas.append( ldda ) + library_dataset = self.get_library_dataset( trans, id=dataset_id, check_ownership=False, check_accessible=True ) + library_datasets.append( library_dataset ) except HTTPBadRequest, e: - raise exceptions.RequestParameterInvalidException( 'Bad Request. ' + str( e.err_msg ) ) + raise exceptions.RequestParameterInvalidException( 'Bad Request.' ) except HTTPInternalServerError, e: - raise exceptions.InternalServerError( 'Internal error. ' + str( e.err_msg ) ) + raise exceptions.InternalServerError( 'Internal error.' ) except Exception, e: - raise exceptions.InternalServerError( 'Unknown error. ' + str( e ) ) + raise exceptions.InternalServerError( 'Unknown error.' ) else: raise exceptions.RequestParameterMissingException( 'Request has to contain a list of dataset ids to download.' ) @@ -580,7 +579,8 @@ raise exceptions.InternalServerError( "Unable to create archive for download." ) composite_extensions = trans.app.datatypes_registry.get_composite_extensions() seen = [] - for ldda in lddas: + for ld in library_datasets: + ldda = ld.library_dataset_dataset_association ext = ldda.extension is_composite = ext in composite_extensions path = "" @@ -669,19 +669,21 @@ archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream elif format == 'uncompressed': - if len(lddas) != 1: + if len(library_datasets) != 1: raise exceptions.RequestParameterInvalidException( "You can download only one uncompressed file at once." ) else: - single_dataset = lddas[ 0 ] - trans.response.set_content_type( single_dataset.get_mime() ) - fStat = os.stat( ldda.file_name ) + single_ld = library_datasets[ 0 ] + ldda = single_ld.library_dataset_dataset_association + dataset = ldda.dataset + fStat = os.stat( dataset.file_name ) + trans.response.set_content_type( ldda.get_mime() ) trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = ldda.name fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname try: - return open( single_dataset.file_name ) + return open( dataset.file_name ) except: raise exceptions.InternalServerError( "This dataset contains no content." ) else: diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -236,9 +236,10 @@ $.fn.refresh_select2 = function() { var select_elt = $(this); - var options = { width: "resolve", + var options = { placeholder:'Click to select', closeOnSelect: !select_elt.is("[MULTIPLE]"), - dropdownAutoWidth : true + dropdownAutoWidth : true, + containerCssClass: 'select2-minwidth' }; return select_elt.select2( options ); } diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -117,7 +117,7 @@ downloadDataset: function(){ var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : this.id}; + var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -275,7 +275,7 @@ } } ); var url = '/api/libraries/datasets/download/' + format; - var data = { 'ldda_ids' : dataset_ids }; + var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return 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"+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset 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data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1232,7 +1232,8 @@ .select2-offscreen,.select2-offscreen:focus{clip:rect(0 0 0 0) !important;width:1px !important;height:1px !important;border:0 !important;margin:0 !important;padding:0 !important;overflow:hidden !important;position:absolute !important;outline:0 !important;left:0px !important;top:0px !important} .select2-display-none{display:none} .select2-measure-scrollbar{position:absolute;top:-10000px;left:-10000px;width:100px;height:100px;overflow:scroll} -@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} +@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.select2-minwidth{min-width:256px} +.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} .galaxy-frame .toggle{color:gold} .galaxy-frame .frame-background{z-index:1000;position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.6;background:#000;overflow:auto} .galaxy-frame .frame-shadow{z-index:1001;position:absolute;display:none;top:0px;left:0px;opacity:0.5;background:#2c3143;border:1px solid #888} diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -16,6 +16,10 @@ @import "select2.less"; + /* fix for zero width select2 - remove when fixed there */ +.select2-minwidth { + min-width: 256px; +} // galaxy sub-components @import "frame.less"; @import "upload.less"; diff -r eb359ebefb58d6b80ab5af14db05843168c428a8 -r 9ebe2f6ecb52702e03c6ef35fe716d70e064578f templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -134,8 +134,8 @@ }); $( '#switch' ).click( function( ev ){ - ##HACK:ity hack hack - ##TODO: remove when out of iframe + //##HACK:ity hack hack + //##TODO: remove when out of iframe var hpanel = Galaxy.currHistoryPanel || ( top.Galaxy && top.Galaxy.currHistoryPanel )? top.Galaxy.currHistoryPanel : null; if( hpanel ){ @@ -163,9 +163,12 @@ }); } - var userIsOwner = ${'true' if user_is_owner else 'false'}, + // use_panels effects where the the center_panel() is rendered: + // w/o it renders to the body, w/ it renders to #center - we need to adjust a few things for scrolling to work + var hasMasthead = ${ 'true' if use_panels else 'false' }, + userIsOwner = ${'true' if user_is_owner else 'false'}, historyJSON = ${h.dumps( history )}, - hdaJSON = ${h.dumps( hdas )}; + hdaJSON = ${h.dumps( hdas )}, panelToUse = ( userIsOwner )? //TODO: change class names ({ location: 'mvc/history/history-panel-edit', className: 'HistoryPanelEdit' }): @@ -176,6 +179,9 @@ })([ 'mvc/user/user-model', panelToUse.location, 'utils/localization' ], function( user, panelMod, _l ){ $(function(){ setUpBehaviors(); + if( hasMasthead ){ + $( '#center' ).css( 'overflow', 'auto' ); + } var panelClass = panelMod[ panelToUse.className ], // history module is already in the dpn chain from the panel. We can re-scope it here. @@ -187,6 +193,7 @@ show_hidden : ${show_hidden_json}, purgeAllowed : Galaxy.config.allow_user_dataset_purge, el : $( "#history-" + historyJSON.id ), + $scrollContainer: hasMasthead? function(){ return this.$el.parent(); } : undefined, model : history }).render(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] 8c25d2: Fix ucsc_build_sites path.
by GitHub 24 Sep '14

24 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8c25d2ae5923874801ea2a334d4b6c6dcdcc88a9 https://github.com/galaxyproject/usegalaxy-playbook/commit/8c25d2ae59238748… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-09-24 (Wed, 24 Sep 2014) Changed paths: M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Fix ucsc_build_sites path.

1 0

commit/galaxy-central: natefoo: Merged in martenson/galaxy-merging/next-stable (pull request #504)
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01f7ec31bc81/ Changeset: 01f7ec31bc81 Branch: next-stable User: natefoo Date: 2014-09-24 15:20:22+00:00 Summary: Merged in martenson/galaxy-merging/next-stable (pull request #504) [NEXT-STABLE] merge of JS changes from #stable Affected #: 13 files diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -9f495158c5ba45fcf61fc37d82aa8545eaba0bd5 latest_2014.08.11 +9f15bf53a11b8a91301381d836271a0ac3b23e71 latest_2014.08.11 diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 client/galaxy/scripts/galaxy.base.js --- a/client/galaxy/scripts/galaxy.base.js +++ b/client/galaxy/scripts/galaxy.base.js @@ -236,9 +236,10 @@ $.fn.refresh_select2 = function() { var select_elt = $(this); - var options = { width: "resolve", + var options = { placeholder:'Click to select', closeOnSelect: !select_elt.is("[MULTIPLE]"), - dropdownAutoWidth : true + dropdownAutoWidth : true, + containerCssClass: 'select2-minwidth' }; return select_elt.select2( options ); } diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 client/galaxy/scripts/mvc/library/library-dataset-view.js --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -117,7 +117,7 @@ downloadDataset: function(){ var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : this.id}; + var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -275,7 +275,7 @@ } } ); var url = '/api/libraries/datasets/download/' + format; - var data = { 'ldda_ids' : dataset_ids }; + var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -518,31 +518,30 @@ :param format: string representing requested archive format :type format: string - :param lddas[]: an array of encoded ids - :type lddas[]: an array + :param ld_ids[]: an array of encoded ids + :type ld_ids[]: an array :rtype: file :returns: either archive with the requested datasets packed inside or a single uncompressed dataset :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound """ - lddas = [] - datasets_to_download = kwd.get( 'ldda_ids%5B%5D', None ) + library_datasets = [] + datasets_to_download = kwd.get( 'ld_ids%5B%5D', None ) if datasets_to_download is None: - datasets_to_download = kwd.get( 'ldda_ids', None ) - + datasets_to_download = kwd.get( 'ld_ids', None ) if ( datasets_to_download is not None ): datasets_to_download = util.listify( datasets_to_download ) for dataset_id in datasets_to_download: try: - ldda = self.get_hda_or_ldda( trans, hda_ldda='ldda', dataset_id=dataset_id ) - lddas.append( ldda ) + library_dataset = self.get_library_dataset( trans, id=dataset_id, check_ownership=False, check_accessible=True ) + library_datasets.append( library_dataset ) except HTTPBadRequest, e: - raise exceptions.RequestParameterInvalidException( 'Bad Request. ' + str( e.err_msg ) ) + raise exceptions.RequestParameterInvalidException( 'Bad Request.' ) except HTTPInternalServerError, e: - raise exceptions.InternalServerError( 'Internal error. ' + str( e.err_msg ) ) + raise exceptions.InternalServerError( 'Internal error.' ) except Exception, e: - raise exceptions.InternalServerError( 'Unknown error. ' + str( e ) ) + raise exceptions.InternalServerError( 'Unknown error.' ) else: raise exceptions.RequestParameterMissingException( 'Request has to contain a list of dataset ids to download.' ) @@ -580,7 +579,8 @@ raise exceptions.InternalServerError( "Unable to create archive for download." ) composite_extensions = trans.app.datatypes_registry.get_composite_extensions() seen = [] - for ldda in lddas: + for ld in library_datasets: + ldda = ld.library_dataset_dataset_association ext = ldda.extension is_composite = ext in composite_extensions path = "" @@ -669,19 +669,21 @@ archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream elif format == 'uncompressed': - if len(lddas) != 1: + if len(library_datasets) != 1: raise exceptions.RequestParameterInvalidException( "You can download only one uncompressed file at once." ) else: - single_dataset = lddas[ 0 ] - trans.response.set_content_type( single_dataset.get_mime() ) - fStat = os.stat( ldda.file_name ) + single_ld = library_datasets[ 0 ] + ldda = single_ld.library_dataset_dataset_association + dataset = ldda.dataset + fStat = os.stat( dataset.file_name ) + trans.response.set_content_type( ldda.get_mime() ) trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = ldda.name fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname try: - return open( single_dataset.file_name ) + return open( dataset.file_name ) except: raise exceptions.InternalServerError( "This dataset contains no content." ) else: diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -236,9 +236,10 @@ $.fn.refresh_select2 = function() { var select_elt = $(this); - var options = { width: "resolve", + var options = { placeholder:'Click to select', closeOnSelect: !select_elt.is("[MULTIPLE]"), - dropdownAutoWidth : true + dropdownAutoWidth : true, + containerCssClass: 'select2-minwidth' }; return select_elt.select2( options ); } diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -117,7 +117,7 @@ downloadDataset: function(){ var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : this.id}; + var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ 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GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var 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.toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1232,7 +1232,8 @@ .select2-offscreen,.select2-offscreen:focus{clip:rect(0 0 0 0) !important;width:1px !important;height:1px !important;border:0 !important;margin:0 !important;padding:0 !important;overflow:hidden !important;position:absolute !important;outline:0 !important;left:0px !important;top:0px !important} .select2-display-none{display:none} .select2-measure-scrollbar{position:absolute;top:-10000px;left:-10000px;width:100px;height:100px;overflow:scroll} -@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} +@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.select2-minwidth{min-width:256px} +.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} .galaxy-frame .toggle{color:gold} .galaxy-frame .frame-background{z-index:1000;position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.6;background:#000;overflow:auto} .galaxy-frame .frame-shadow{z-index:1001;position:absolute;display:none;top:0px;left:0px;opacity:0.5;background:#2c3143;border:1px solid #888} diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -16,6 +16,10 @@ @import "select2.less"; + /* fix for zero width select2 - remove when fixed there */ +.select2-minwidth { + min-width: 256px; +} // galaxy sub-components @import "frame.less"; @import "upload.less"; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4587dfcf869d/ Changeset: 4587dfcf869d Branch: next-stable User: martenson Date: 2014-09-23 14:56:26+00:00 Summary: trying to merge stable->next stable, this should take care of changes due to build process affecting the stable commit Affected #: 12 files diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 client/galaxy/scripts/galaxy.base.js --- a/client/galaxy/scripts/galaxy.base.js +++ b/client/galaxy/scripts/galaxy.base.js @@ -236,9 +236,10 @@ $.fn.refresh_select2 = function() { var select_elt = $(this); - var options = { width: "resolve", + var options = { placeholder:'Click to select', closeOnSelect: !select_elt.is("[MULTIPLE]"), - dropdownAutoWidth : true + dropdownAutoWidth : true, + containerCssClass: 'select2-minwidth' }; return select_elt.select2( options ); } diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 client/galaxy/scripts/mvc/library/library-dataset-view.js --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -117,7 +117,7 @@ downloadDataset: function(){ var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : this.id}; + var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -275,7 +275,7 @@ } } ); var url = '/api/libraries/datasets/download/' + format; - var data = { 'ldda_ids' : dataset_ids }; + var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -518,31 +518,30 @@ :param format: string representing requested archive format :type format: string - :param lddas[]: an array of encoded ids - :type lddas[]: an array + :param ld_ids[]: an array of encoded ids + :type ld_ids[]: an array :rtype: file :returns: either archive with the requested datasets packed inside or a single uncompressed dataset :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound """ - lddas = [] - datasets_to_download = kwd.get( 'ldda_ids%5B%5D', None ) + library_datasets = [] + datasets_to_download = kwd.get( 'ld_ids%5B%5D', None ) if datasets_to_download is None: - datasets_to_download = kwd.get( 'ldda_ids', None ) - + datasets_to_download = kwd.get( 'ld_ids', None ) if ( datasets_to_download is not None ): datasets_to_download = util.listify( datasets_to_download ) for dataset_id in datasets_to_download: try: - ldda = self.get_hda_or_ldda( trans, hda_ldda='ldda', dataset_id=dataset_id ) - lddas.append( ldda ) + library_dataset = self.get_library_dataset( trans, id=dataset_id, check_ownership=False, check_accessible=True ) + library_datasets.append( library_dataset ) except HTTPBadRequest, e: - raise exceptions.RequestParameterInvalidException( 'Bad Request. ' + str( e.err_msg ) ) + raise exceptions.RequestParameterInvalidException( 'Bad Request.' ) except HTTPInternalServerError, e: - raise exceptions.InternalServerError( 'Internal error. ' + str( e.err_msg ) ) + raise exceptions.InternalServerError( 'Internal error.' ) except Exception, e: - raise exceptions.InternalServerError( 'Unknown error. ' + str( e ) ) + raise exceptions.InternalServerError( 'Unknown error.' ) else: raise exceptions.RequestParameterMissingException( 'Request has to contain a list of dataset ids to download.' ) @@ -580,7 +579,8 @@ raise exceptions.InternalServerError( "Unable to create archive for download." ) composite_extensions = trans.app.datatypes_registry.get_composite_extensions() seen = [] - for ldda in lddas: + for ld in library_datasets: + ldda = ld.library_dataset_dataset_association ext = ldda.extension is_composite = ext in composite_extensions path = "" @@ -669,19 +669,21 @@ archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream elif format == 'uncompressed': - if len(lddas) != 1: + if len(library_datasets) != 1: raise exceptions.RequestParameterInvalidException( "You can download only one uncompressed file at once." ) else: - single_dataset = lddas[ 0 ] - trans.response.set_content_type( single_dataset.get_mime() ) - fStat = os.stat( ldda.file_name ) + single_ld = library_datasets[ 0 ] + ldda = single_ld.library_dataset_dataset_association + dataset = ldda.dataset + fStat = os.stat( dataset.file_name ) + trans.response.set_content_type( ldda.get_mime() ) trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = ldda.name fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname try: - return open( single_dataset.file_name ) + return open( dataset.file_name ) except: raise exceptions.InternalServerError( "This dataset contains no content." ) else: diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -236,9 +236,10 @@ $.fn.refresh_select2 = function() { var select_elt = $(this); - var options = { width: "resolve", + var options = { placeholder:'Click to select', closeOnSelect: !select_elt.is("[MULTIPLE]"), - dropdownAutoWidth : true + dropdownAutoWidth : true, + containerCssClass: 'select2-minwidth' }; return select_elt.select2( options ); } diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -117,7 +117,7 @@ downloadDataset: function(){ var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : this.id}; + var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ 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GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var 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[title]").tooltip({placement:"bottom"});$("[title]").tooltip()}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 static/scripts/packed/mvc/library/library-dataset-view.js --- a/static/scripts/packed/mvc/library/library-dataset-view.js +++ b/static/scripts/packed/mvc/library/library-dataset-view.js @@ -1,1 +1,1 @@ -define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click 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Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ldda_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1232,7 +1232,8 @@ .select2-offscreen,.select2-offscreen:focus{clip:rect(0 0 0 0) !important;width:1px !important;height:1px !important;border:0 !important;margin:0 !important;padding:0 !important;overflow:hidden !important;position:absolute !important;outline:0 !important;left:0px !important;top:0px !important} .select2-display-none{display:none} .select2-measure-scrollbar{position:absolute;top:-10000px;left:-10000px;width:100px;height:100px;overflow:scroll} -@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} +@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.select2-minwidth{min-width:256px} +.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} .galaxy-frame .toggle{color:gold} .galaxy-frame .frame-background{z-index:1000;position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.6;background:#000;overflow:auto} .galaxy-frame .frame-shadow{z-index:1001;position:absolute;display:none;top:0px;left:0px;opacity:0.5;background:#2c3143;border:1px solid #888} diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -16,6 +16,10 @@ @import "select2.less"; + /* fix for zero width select2 - remove when fixed there */ +.select2-minwidth { + min-width: 256px; +} // galaxy sub-components @import "frame.less"; @import "upload.less"; https://bitbucket.org/galaxy/galaxy-central/commits/634a8a8e9916/ Changeset: 634a8a8e9916 Branch: next-stable User: martenson Date: 2014-09-23 14:59:49+00:00 Summary: merge stable into next-stable Affected #: 13 files diff -r 4587dfcf869da7f7f6bcd83511016d67a08daed8 -r 634a8a8e99163367dd3df11650aba7aef1166324 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -9f495158c5ba45fcf61fc37d82aa8545eaba0bd5 latest_2014.08.11 +9f15bf53a11b8a91301381d836271a0ac3b23e71 latest_2014.08.11 https://bitbucket.org/galaxy/galaxy-central/commits/01f7ec31bc81/ Changeset: 01f7ec31bc81 Branch: next-stable User: natefoo Date: 2014-09-24 15:20:22+00:00 Summary: Merged in martenson/galaxy-merging/next-stable (pull request #504) [NEXT-STABLE] merge of JS changes from #stable Affected #: 13 files diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -9f495158c5ba45fcf61fc37d82aa8545eaba0bd5 latest_2014.08.11 +9f15bf53a11b8a91301381d836271a0ac3b23e71 latest_2014.08.11 diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 client/galaxy/scripts/galaxy.base.js --- a/client/galaxy/scripts/galaxy.base.js +++ b/client/galaxy/scripts/galaxy.base.js @@ -236,9 +236,10 @@ $.fn.refresh_select2 = function() { var select_elt = $(this); - var options = { width: "resolve", + var options = { placeholder:'Click to select', closeOnSelect: !select_elt.is("[MULTIPLE]"), - dropdownAutoWidth : true + dropdownAutoWidth : true, + containerCssClass: 'select2-minwidth' }; return select_elt.select2( options ); } diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 client/galaxy/scripts/mvc/library/library-dataset-view.js --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -117,7 +117,7 @@ downloadDataset: function(){ var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : this.id}; + var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -275,7 +275,7 @@ } } ); var url = '/api/libraries/datasets/download/' + format; - var data = { 'ldda_ids' : dataset_ids }; + var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -518,31 +518,30 @@ :param format: string representing requested archive format :type format: string - :param lddas[]: an array of encoded ids - :type lddas[]: an array + :param ld_ids[]: an array of encoded ids + :type ld_ids[]: an array :rtype: file :returns: either archive with the requested datasets packed inside or a single uncompressed dataset :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound """ - lddas = [] - datasets_to_download = kwd.get( 'ldda_ids%5B%5D', None ) + library_datasets = [] + datasets_to_download = kwd.get( 'ld_ids%5B%5D', None ) if datasets_to_download is None: - datasets_to_download = kwd.get( 'ldda_ids', None ) - + datasets_to_download = kwd.get( 'ld_ids', None ) if ( datasets_to_download is not None ): datasets_to_download = util.listify( datasets_to_download ) for dataset_id in datasets_to_download: try: - ldda = self.get_hda_or_ldda( trans, hda_ldda='ldda', dataset_id=dataset_id ) - lddas.append( ldda ) + library_dataset = self.get_library_dataset( trans, id=dataset_id, check_ownership=False, check_accessible=True ) + library_datasets.append( library_dataset ) except HTTPBadRequest, e: - raise exceptions.RequestParameterInvalidException( 'Bad Request. ' + str( e.err_msg ) ) + raise exceptions.RequestParameterInvalidException( 'Bad Request.' ) except HTTPInternalServerError, e: - raise exceptions.InternalServerError( 'Internal error. ' + str( e.err_msg ) ) + raise exceptions.InternalServerError( 'Internal error.' ) except Exception, e: - raise exceptions.InternalServerError( 'Unknown error. ' + str( e ) ) + raise exceptions.InternalServerError( 'Unknown error.' ) else: raise exceptions.RequestParameterMissingException( 'Request has to contain a list of dataset ids to download.' ) @@ -580,7 +579,8 @@ raise exceptions.InternalServerError( "Unable to create archive for download." ) composite_extensions = trans.app.datatypes_registry.get_composite_extensions() seen = [] - for ldda in lddas: + for ld in library_datasets: + ldda = ld.library_dataset_dataset_association ext = ldda.extension is_composite = ext in composite_extensions path = "" @@ -669,19 +669,21 @@ archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream elif format == 'uncompressed': - if len(lddas) != 1: + if len(library_datasets) != 1: raise exceptions.RequestParameterInvalidException( "You can download only one uncompressed file at once." ) else: - single_dataset = lddas[ 0 ] - trans.response.set_content_type( single_dataset.get_mime() ) - fStat = os.stat( ldda.file_name ) + single_ld = library_datasets[ 0 ] + ldda = single_ld.library_dataset_dataset_association + dataset = ldda.dataset + fStat = os.stat( dataset.file_name ) + trans.response.set_content_type( ldda.get_mime() ) trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' fname = ldda.name fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname try: - return open( single_dataset.file_name ) + return open( dataset.file_name ) except: raise exceptions.InternalServerError( "This dataset contains no content." ) else: diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -236,9 +236,10 @@ $.fn.refresh_select2 = function() { var select_elt = $(this); - var options = { width: "resolve", + var options = { placeholder:'Click to select', closeOnSelect: !select_elt.is("[MULTIPLE]"), - dropdownAutoWidth : true + dropdownAutoWidth : true, + containerCssClass: 'select2-minwidth' }; return select_elt.select2( options ); } diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/mvc/library/library-dataset-view.js --- a/static/scripts/mvc/library/library-dataset-view.js +++ b/static/scripts/mvc/library/library-dataset-view.js @@ -117,7 +117,7 @@ downloadDataset: function(){ var url = '/api/libraries/datasets/download/uncompressed'; - var data = {'ldda_ids' : this.id}; + var data = {'ld_ids' : this.id}; this.processDownload(url, data); }, diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -275,7 +275,7 @@ } } ); var url = '/api/libraries/datasets/download/' + format; - var data = { 'ldda_ids' : dataset_ids }; + var data = { 'ld_ids' : dataset_ids }; this.processDownload( url, data, 'get' ); }, diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a<c.length&&!window.requestAnimationFrame;++a){window.requestAnimationFrame=window[c[a]+"RequestAnimationFrame"];window.cancelRequestAnimationFrame=window[c[a]+"CancelRequestAnimationFrame"]}if(!window.requestAnimationFrame){window.requestAnimationFrame=function(h,e){var d=new Date().getTime();var f=Math.max(0,16-(d-b));var g=window.setTimeout(function(){h(d+f)},f);b=d+f;return 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"+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a 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permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset 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data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(d,c,b){var a=Backbone.View.extend({el:"#center",model:null,options:{},events:{"click .toolbtn_modify_dataset":"enableModification","click .toolbtn_cancel_modifications":"render","click .toolbtn-download-dataset":"downloadDataset","click .toolbtn-import-dataset":"importIntoHistory","click .toolbtn-share-dataset":"shareDataset","click .btn-copy-link-to-clipboard":"copyToClipboard","click .btn-make-private":"makeDatasetPrivate","click .btn-remove-restrictions":"removeDatasetRestrictions","click .toolbtn_save_permissions":"savePermissions","click .toolbtn_save_modifications":"comingSoon",},initialize:function(e){this.options=_.extend(this.options,e);if(this.options.id){this.fetchDataset()}},fetchDataset:function(e){this.options=_.extend(this.options,e);this.model=new c.Item({id:this.options.id});var f=this;this.model.fetch({success:function(){if(f.options.show_permissions){f.showPermissions()}else{if(f.options.show_version){f.fetchVersion()}else{f.render()}}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg+" Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}else{d.error("An error ocurred. Click this to go back.","",{onclick:function(){Galaxy.libraries.library_router.back()}})}}})},render:function(e){this.options=_.extend(this.options,e);$(".tooltip").remove();var f=this.templateDataset();this.$el.html(f({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},fetchVersion:function(e){this.options=_.extend(this.options,e);that=this;if(!this.options.ldda_id){this.render();d.error("Library dataset version requested but no id provided.")}else{this.ldda=new c.Ldda({id:this.options.ldda_id});this.ldda.url=this.ldda.urlRoot+this.model.id+"/versions/"+this.ldda.id;this.ldda.fetch({success:function(){that.renderVersion()},error:function(g,f){if(typeof f.responseJSON!=="undefined"){d.error(f.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})}},renderVersion:function(){$(".tooltip").remove();var e=this.templateVersion();this.$el.html(e({item:this.model,ldda:this.ldda}));$(".peek").html(this.ldda.get("peek"))},enableModification:function(){$(".tooltip").remove();var e=this.templateModifyDataset();this.$el.html(e({item:this.model}));$(".peek").html(this.model.get("peek"));$("#center [data-toggle]").tooltip()},downloadDataset:function(){var e="/api/libraries/datasets/download/uncompressed";var f={ld_ids:this.id};this.processDownload(e,f)},processDownload:function(f,g,h){if(f&&g){g=typeof g=="string"?g:$.param(g);var e="";$.each(g.split("&"),function(){var i=this.split("=");e+='<input type="hidden" name="'+i[0]+'" value="'+i[1]+'" />'});$('<form action="'+f+'" method="'+(h||"post")+'">'+e+"</form>").appendTo("body").submit().remove();d.info("Your download will begin soon.")}},importIntoHistory:function(){this.refreshUserHistoriesList(function(e){var f=e.templateBulkImportInModal();e.modal=Galaxy.modal;e.modal.show({closing_events:true,title:"Import into History",body:f({histories:e.histories.models}),buttons:{Import:function(){e.importCurrentIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})},refreshUserHistoriesList:function(f){var e=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(g){if(g.length===0){d.warning("You have to create history first. Click this to do so.","",{onclick:function(){window.location="/"}})}else{f(e)}},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error(g.responseJSON.err_msg)}else{d.error("An error ocurred.")}}})},importCurrentIntoHistory:function(){var e=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();var f=new c.HistoryItem();f.url=f.urlRoot+e+"/contents";jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+e);f.save({content:this.id,source:"library"},{success:function(){Galaxy.modal.hide();d.success("Dataset imported. Click this to start analysing it.","",{onclick:function(){window.location="/"}})},error:function(h,g){if(typeof g.responseJSON!=="undefined"){d.error("Dataset not imported. "+g.responseJSON.err_msg)}else{d.error("An error occured. Dataset not imported. Please try again.")}}})},shareDataset:function(){d.info("Feature coming soon.")},goBack:function(){Galaxy.libraries.library_router.back()},showPermissions:function(f){this.options=_.extend(this.options,f);$(".tooltip").remove();if(this.options.fetched_permissions!==undefined){if(this.options.fetched_permissions.access_dataset_roles.length===0){this.model.set({is_unrestricted:true})}else{this.model.set({is_unrestricted:false})}}var h=false;if(Galaxy.currUser){h=Galaxy.currUser.isAdmin()}var g=this.templateDatasetPermissions();this.$el.html(g({item:this.model,is_admin:h}));var e=this;if(this.options.fetched_permissions===undefined){$.get("/api/libraries/datasets/"+e.id+"/permissions?scope=current").done(function(i){e.prepareSelectBoxes({fetched_permissions:i,is_admin:h})}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}else{this.prepareSelectBoxes({is_admin:h})}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},prepareSelectBoxes:function(r){this.options=_.extend(this.options,r);var s=this.options.fetched_permissions;var k=this.options.is_admin;var q=this;var m=[];for(var h=0;h<s.access_dataset_roles.length;h++){m.push(s.access_dataset_roles[h]+":"+s.access_dataset_roles[h])}var f=[];for(var h=0;h<s.modify_item_roles.length;h++){f.push(s.modify_item_roles[h]+":"+s.modify_item_roles[h])}var g=[];for(var h=0;h<s.manage_dataset_roles.length;h++){g.push(s.manage_dataset_roles[h]+":"+s.manage_dataset_roles[h])}if(k){var o={minimumInputLength:0,css:"access_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#access_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:m.join(","),dropdownCssClass:"bigdrop"};var l={minimumInputLength:0,css:"modify_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#modify_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:f.join(","),dropdownCssClass:"bigdrop"};var p={minimumInputLength:0,css:"manage_perm",multiple:true,placeholder:"Click to select a role",container:q.$el.find("#manage_perm"),ajax:{url:"/api/libraries/datasets/"+q.id+"/permissions?scope=available",dataType:"json",quietMillis:100,data:function(i,t){return{q:i,page_limit:10,page:t}},results:function(u,t){var i=(t*10)<u.total;return{results:u.roles,more:i}}},formatResult:function j(i){return i.name+" type: "+i.type},formatSelection:function e(i){return i.name},initSelection:function(i,u){var t=[];$(i.val().split(",")).each(function(){var v=this.split(":");t.push({id:v[1],name:v[1]})});u(t)},initialData:g.join(","),dropdownCssClass:"bigdrop"};q.accessSelectObject=new b.View(o);q.modifySelectObject=new b.View(l);q.manageSelectObject=new b.View(p)}else{var n=q.templateAccessSelect();$.get("/api/libraries/datasets/"+q.id+"/permissions?scope=available",function(i){$(".access_perm").html(n({options:i.roles}));q.accessSelectObject=$("#access_select").select2()}).fail(function(){d.error("An error occurred while attempting to fetch dataset permissions.")})}},comingSoon:function(){d.warning("Feature coming soon.")},copyToClipboard:function(){var e=Backbone.history.location.href;if(e.lastIndexOf("/permissions")!==-1){e=e.substr(0,e.lastIndexOf("/permissions"))}window.prompt("Copy to clipboard: Ctrl+C, Enter",e)},makeDatasetPrivate:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=make_private").done(function(f){e.model.set({is_unrestricted:false});e.showPermissions({fetched_permissions:f});d.success("The dataset is now private to you.")}).fail(function(){d.error("An error occurred while attempting to make dataset private.")})},removeDatasetRestrictions:function(){var e=this;$.post("/api/libraries/datasets/"+e.id+"/permissions?action=remove_restrictions").done(function(f){e.model.set({is_unrestricted:true});e.showPermissions({fetched_permissions:f});d.success("Access to this dataset is now unrestricted.")}).fail(function(){d.error("An error occurred while attempting to make dataset unrestricted.")})},savePermissions:function(e){var n=this;var k=this.accessSelectObject.$el.select2("data");var f=this.manageSelectObject.$el.select2("data");var m=this.modifySelectObject.$el.select2("data");var g=[];var j=[];var l=[];for(var h=k.length-1;h>=0;h--){g.push(k[h].id)}for(var h=f.length-1;h>=0;h--){j.push(f[h].id)}for(var h=m.length-1;h>=0;h--){l.push(m[h].id)}$.post("/api/libraries/datasets/"+n.id+"/permissions?action=set_permissions",{"access_ids[]":g,"manage_ids[]":j,"modify_ids[]":l,}).done(function(i){n.showPermissions({fetched_permissions:i});d.success("Permissions saved.")}).fail(function(){d.error("An error occurred while attempting to set dataset permissions.")})},templateDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Download dataset" class="btn btn-default toolbtn-download-dataset primary-button" type="button"><span class="fa fa-download"></span> Download</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Import dataset into history" class="btn btn-default toolbtn-import-dataset primary-button" type="button"><span class="fa fa-book"></span> to History</span></button>');e.push(' <% if (item.get("can_user_modify")) { %>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library item" class="btn btn-default toolbtn_modify_dataset primary-button" type="button"><span class="fa fa-pencil"></span> Modify</span></button>');e.push(" <% } %>");e.push(' <% if (item.get("can_user_manage")) { %>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage permissions" class="btn btn-default toolbtn_change_permissions primary-button" type="button"><span class="fa fa-group"></span> Permissions</span></button></a>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Share dataset" class="btn btn-default toolbtn-share-dataset primary-button" type="button"><span class="fa fa-share"></span> Share</span></button>');e.push(" <% } %>");e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<% if (item.get("is_unrestricted")) { %>');e.push(' <div class="alert alert-info">');e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"></span> To Clipboard</span></button> ');e.push(" </div>");e.push("<% } %>");e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><%= _.escape(item.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (item.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (item.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push(' <% if (item.get("has_versions")) { %>');e.push(" <div>");e.push(" <h3>Expired versions:</h3>");e.push(" <ul>");e.push(' <% _.each(item.get("expired_versions"), function(version) { %>');e.push(' <li><a title="See details of this version" href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>/versions/<%- version[0] %>"><%- version[1] %></a></li>');e.push(" <% }) %>");e.push(" <ul>");e.push(" </div>");e.push(" <% } %>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateVersion:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go to latest dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-caret-left fa-lg"></span> Latest dataset</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push(' <div class="alert alert-warning">This is an expired version of the library dataset: <%= _.escape(item.get("name")) %></div>');e.push('<div class="dataset_table">');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(ldda.id) %>">Name</th>');e.push(' <td><%= _.escape(ldda.get("name")) %></td>');e.push(" </tr>");e.push(' <% if (ldda.get("file_ext")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(ldda.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("genome_build")) { %>');e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(ldda.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("file_size")) { %>');e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(ldda.get("file_size")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("date_uploaded")) { %>');e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(ldda.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("uploaded_by")) { %>');e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(ldda.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_data_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_comment_lines")) { %>');e.push(" <tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_comment_lines")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_columns")) { %>');e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("metadata_column_types")) { %>');e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("message")) { %>');e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("message")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_blurb")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(' <% if (ldda.get("misc_info")) { %>');e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(ldda.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <% } %>");e.push(" </table>");e.push(" <div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push(" </div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateModifyDataset:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <button data-toggle="tooltip" data-placement="top" title="Cancel modifications" class="btn btn-default toolbtn_cancel_modifications primary-button" type="button"><span class="fa fa-times"></span> Cancel</span></button>');e.push(' <button data-toggle="tooltip" data-placement="top" title="Save modifications" class="btn btn-default toolbtn_save_modifications primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<div class="dataset_table">');e.push('<p>For more editing options please import the dataset to history and use "Edit attributes" on it.</p>');e.push(' <table class="grid table table-striped table-condensed">');e.push(" <tr>");e.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');e.push(' <td><input class="input_dataset_name form-control" type="text" placeholder="name" value="<%= _.escape(item.get("name")) %>"></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Data type</th>');e.push(' <td><%= _.escape(item.get("file_ext")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Genome build</th>');e.push(' <td><%= _.escape(item.get("genome_build")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Size</th>');e.push(' <td><%= _.escape(item.get("file_size")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Date uploaded (UTC)</th>');e.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Uploaded by</th>');e.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');e.push(" </tr>");e.push(' <tr scope="row">');e.push(' <th scope="row">Data Lines</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');e.push(" </tr>");e.push(' <th scope="row">Comment Lines</th>');e.push(' <% if (item.get("metadata_comment_lines") === "") { %>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');e.push(" <% } else { %>");e.push(' <td scope="row">unknown</td>');e.push(" <% } %>");e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Number of Columns</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Column Types</th>');e.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Message</th>');e.push(' <td scope="row"><%= _.escape(item.get("message")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous information</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_info")) %></td>');e.push(" </tr>");e.push(" <tr>");e.push(' <th scope="row">Miscellaneous blurb</th>');e.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');e.push(" </tr>");e.push(" </table>");e.push("<div>");e.push(' <pre class="peek">');e.push(" </pre>");e.push("</div>");e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateDatasetPermissions:function(){var e=[];e.push('<div class="library_style_container">');e.push(' <div id="library_toolbar">');e.push(' <a href="#folders/<%- item.get("folder_id") %>"><button data-toggle="tooltip" data-placement="top" title="Go back to containing folder" class="btn btn-default primary-button" type="button"><span class="fa fa-folder-open-o"></span> Containing Folder</span></button></a>');e.push(' <a href="#folders/<%- item.get("folder_id") %>/datasets/<%- item.id %>"><button data-toggle="tooltip" data-placement="top" title="Go back to dataset" class="btn btn-default primary-button" type="button"><span class="fa fa-file-o"></span> Dataset Details</span></button><a>');e.push(" </div>");e.push('<ol class="breadcrumb">');e.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');e.push(' <% _.each(item.get("full_path"), function(path_item) { %>');e.push(" <% if (path_item[0] != item.id) { %>");e.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');e.push("<% } else { %>");e.push(' <li class="active"><span title="You are here"><%- path_item[1] %></span></li>');e.push(" <% } %>");e.push(" <% }); %>");e.push("</ol>");e.push('<h1>Dataset: <%= _.escape(item.get("name")) %></h1>');e.push('<div class="alert alert-warning">');e.push("<% if (is_admin) { %>");e.push("You are logged in as an <strong>administrator</strong> therefore you can manage any dataset on this Galaxy instance. Please make sure you understand the consequences.");e.push("<% } else { %>");e.push("You can assign any number of roles to any of the following permission types. However please read carefully the implications of such actions.");e.push("<% } %>");e.push("</div>");e.push('<div class="dataset_table">');e.push("<h2>Library-related permissions</h2>");e.push("<h4>Roles that can modify the library item</h4>");e.push('<div id="modify_perm" class="modify_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can modify name, metadata, and other information about this library item.</div>');e.push("<hr/>");e.push("<h2>Dataset-related permissions</h2>");e.push('<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>');e.push('<% if (!item.get("is_unrestricted")) { %>');e.push(" <p>You can remove all access restrictions on this dataset. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Everybody will be able to access the dataset." class="btn btn-default btn-remove-restrictions primary-button" type="button">');e.push(' <span class="fa fa-globe"> Remove restrictions</span>');e.push(" </button>");e.push(" </p>");e.push("<% } else { %>");e.push(" This dataset is unrestricted so everybody can access it. Just share the URL of this page.");e.push(' <button data-toggle="tooltip" data-placement="top" title="Copy to clipboard" class="btn btn-default btn-copy-link-to-clipboard primary-button" type="button"><span class="fa fa-clipboard"> To Clipboard</span></button> ');e.push(" <p>You can make this dataset private to you. ");e.push(' <button data-toggle="tooltip" data-placement="top" title="Only you will be able to access the dataset." class="btn btn-default btn-make-private primary-button" type="button"><span class="fa fa-key"> Make Private</span></button>');e.push(" </p>");e.push("<% } %>");e.push("<h4>Roles that can access the dataset</h4>");e.push('<div id="access_perm" class="access_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User has to have <strong>all these roles</strong> in order to access this dataset. Users without access permission <strong>cannot</strong> have other permissions on this dataset. If there are no access roles set on the dataset it is considered <strong>unrestricted</strong>.</div>');e.push("<h4>Roles that can manage permissions on the dataset</h4>");e.push('<div id="manage_perm" class="manage_perm roles-selection"></div>');e.push('<div class="alert alert-info roles-selection">User with <strong>any</strong> of these roles can manage permissions of this dataset. If you remove yourself you will loose the ability manage this dataset unless you are an admin.</div>');e.push('<button data-toggle="tooltip" data-placement="top" title="Save modifications made on this page" class="btn btn-default toolbtn_save_permissions primary-button" type="button"><span class="fa fa-floppy-o"></span> Save</span></button>');e.push("</div>");e.push("</div>");return _.template(e.join(""))},templateBulkImportInModal:function(){var e=[];e.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');e.push("Select history: ");e.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');e.push(" <% _.each(histories, function(history) { %>");e.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');e.push(" <% }); %>");e.push("</select>");e.push("</span>");return _.template(e.join(""))},templateAccessSelect:function(){var e=[];e.push('<select id="access_select" multiple>');e.push(" <% _.each(options, function(option) { %>");e.push(' <option value="<%- option.name %>"><%- option.name %></option>');e.push(" <% }); %>");e.push("</select>");return _.template(e.join(""))}});return{LibraryDatasetView:a}}); \ No newline at end of file diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ldda_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/ui/ui-select"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_show_libinfo":"showLibInfo","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0},disabled_jstree_element:"folders"},modal:null,jstree:null,histories:null,select_genome:null,select_extension:null,list_extensions:[],auto:{id:"auto",text:"Auto-detect",description:"This system will try to detect the file type automatically. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems (e.g., different number of columns on different rows). You can still coerce the system to set your data to the format you think it should be. You can also upload compressed files, which will automatically be decompressed."},list_genomes:[],initialize:function(g){this.options=_.defaults(g||{},this.defaults);this.fetchExtAndGenomes();this.render()},render:function(g){this.options=_.extend(this.options,g);var i=this.templateToolBar();var h={id:this.options.id,is_admin:false,is_anonym:true,user_library_import_dir:Galaxy.config.user_library_import_dir,allow_library_path_paste:Galaxy.config.allow_library_path_paste,library_import_dir:Galaxy.config.library_import_dir,mutiple_add_dataset_options:false};if(Galaxy.currUser){h.is_admin=Galaxy.currUser.isAdmin();h.is_anonym=Galaxy.currUser.isAnonymous();if(h.user_library_import_dir!==null||h.allow_library_path_paste!==false||h.library_import_dir!==null){h.mutiple_add_dataset_options=true}}this.$el.html(i(h))},configureElements:function(g){this.options=_.extend(this.options,g);if(this.options.can_add_library_item===true){$(".add-library-items").show()}else{$(".add-library-items").hide()}if(this.options.contains_file===true){if(Galaxy.currUser){if(!Galaxy.currUser.isAnonymous()){$(".logged-dataset-manipulation").show();$(".dataset-manipulation").show()}else{$(".dataset-manipulation").show();$(".logged-dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}}else{$(".logged-dataset-manipulation").hide();$(".dataset-manipulation").hide()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(i){i.preventDefault();i.stopPropagation();var g=this;var h=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:h(),buttons:{Create:function(){g.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var g=this.serialize_new_folder();if(this.validate_new_folder(g)){var h=new d.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;h.save(g,{success:function(i){Galaxy.modal.hide();f.success("Folder created.");i.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(i)},error:function(j,i){Galaxy.modal.hide();if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}else{f.error("Folder's name is missing.")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(g){return g.name!==""},modalBulkImport:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select some datasets first.")}else{this.refreshUserHistoriesList(function(i){var h=i.templateBulkImportInModal();i.modal=Galaxy.modal;i.modal.show({closing_events:true,title:"Import into History",body:h({histories:i.histories.models}),buttons:{Import:function(){i.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(h){var g=this;this.histories=new d.GalaxyHistories();this.histories.fetch({success:function(){h(g)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var k=$("select[name=dataset_import_bulk] option:selected").val();var n=$("select[name=dataset_import_bulk] option:selected").text();this.options.last_used_history_id=k;var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var m=[];for(var j=h.length-1;j>=0;j--){var g=h[j];var l=new d.HistoryItem();l.url=l.urlRoot+k+"/contents";l.content=g;l.source="library";m.push(l)}this.initChainCallControl({length:m.length,action:"to_history",history_name:n});jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+k);this.chainCallImportingIntoHistory(m,n)},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(g,k){var i=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){i.push(this.parentElement.parentElement.id)}});var h="/api/libraries/datasets/download/"+k;var j={ld_ids:i};this.processDownload(h,j,"get")},processDownload:function(h,i,j){if(h&&i){i=typeof i==="string"?i:$.param(i);var g="";$.each(i.split("&"),function(){var k=this.split("=");g+='<input type="hidden" name="'+k[0]+'" value="'+k[1]+'" />'});$('<form action="'+h+'" method="'+(j||"post")+'">'+g+"</form>").appendTo("body").submit().remove();f.info("Your download will begin soon.")}else{f.error("An error occurred.")}},addFilesFromHistoryModal:function(){this.refreshUserHistoriesList(function(g){g.modal=Galaxy.modal;var h=g.templateAddFilesFromHistory();var i=g.options.full_path[g.options.full_path.length-1][1];g.modal.show({closing_events:true,title:"Adding datasets from your history to folder "+i,body:h({histories:g.histories.models}),buttons:{Add:function(){g.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.back()}});if(g.histories.models.length>0){g.fetchAndDisplayHistoryContents(g.histories.models[0].id);$("#dataset_add_bulk").change(function(j){g.fetchAndDisplayHistoryContents(j.target.value)})}else{f.error("An error ocurred.")}})},importFilesFromPathModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateImportPathModal();this.modal.show({closing_events:true,title:"Please enter paths to import",body:g({}),buttons:{Import:function(){h.importFromPathsClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes()},fetchExtAndGenomes:function(){var g=this;e.get(galaxy_config.root+"api/datatypes?extension_only=False",function(h){for(key in h){g.list_extensions.push({id:h[key].extension,text:h[key].extension,description:h[key].description,description_url:h[key].description_url})}g.list_extensions.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0});g.list_extensions.unshift(g.auto)});e.get(galaxy_config.root+"api/genomes",function(h){for(key in h){g.list_genomes.push({id:h[key][1],text:h[key][0]})}g.list_genomes.sort(function(j,i){return j.id>i.id?1:j.id<i.id?-1:0})})},renderSelectBoxes:function(){var g=this;this.select_genome=new a.View({css:"genome",data:g.list_genomes,container:Galaxy.modal.$el.find("#genome"),value:"?"});this.select_extension=new a.View({css:"extension",data:g.list_extensions,container:Galaxy.modal.$el.find("#extension"),value:"auto"})},importFilesFromUserdirModal:function(){var h=this;this.modal=Galaxy.modal;var g=this.templateBrowserModal();this.modal.show({closing_events:true,title:"Please select folders or files",body:g({}),buttons:{Import:function(){h.importFromUserdirClicked(h)},Close:function(){Galaxy.modal.hide()}},closing_callback:function(){Galaxy.libraries.library_router.navigate("folders/"+h.id,{trigger:true})}});this.renderSelectBoxes();this.renderJstree({disabled_jstree_element:"folders"});$("input[type=radio]").change(function(i){if(i.target.value==="jstree-disable-folders"){h.renderJstree({disabled_jstree_element:"folders"});$(".jstree-folders-message").hide();$(".jstree-preserve-structure").hide();$(".jstree-link-files").hide();$(".jstree-files-message").show()}else{if(i.target.value==="jstree-disable-files"){$(".jstree-files-message").hide();$(".jstree-folders-message").show();$(".jstree-link-files").show();$(".jstree-preserve-structure").show();h.renderJstree({disabled_jstree_element:"files"})}}})},renderJstree:function(g){var i=this;this.options=_.extend(this.options,g);var h=this.options.disabled_jstree_element;this.jstree=new d.Jstree();this.jstree.url=this.jstree.urlRoot+"?target=userdir&format=jstree&disable="+h;this.jstree.fetch({success:function(k,j){define("jquery",function(){return jQuery});require(["libs/jquery/jstree"],function(l){$("#jstree_browser").jstree("destroy");$("#jstree_browser").jstree({core:{data:k},plugins:["types","checkbox"],types:{folder:{icon:"jstree-folder"},file:{icon:"jstree-file"}},checkbox:{three_state:false}})})},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},importFromPathsClicked:function(){var g=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var j=this.select_genome.value();var m=$("textarea#import_paths").val();var l=[];if(!m){f.info("Please enter a path relative to Galaxy root.")}else{this.modal.disableButton("Import");m=m.split("\n");for(var k=m.length-1;k>=0;k--){trimmed=m[k].trim();if(trimmed.length!==0){l.push(trimmed)}}this.initChainCallControl({length:l.length,action:"adding_datasets"});this.chainCallImportingFolders({paths:l,preserve_dirs:g,link_data:n,source:"admin_path",file_type:h,dbkey:j})}},initChainCallControl:function(g){var h;switch(g.action){case"adding_datasets":h=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h({folder_name:this.options.folder_name}));break;case"deleting_datasets":h=this.templateDeletingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(h());break;case"to_history":h=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(h({history_name:g.history_name}));break;default:console.error("Wrong action specified.");break}this.progress=0;this.progressStep=100/g.length;this.options.chain_call_control.total_number=g.length;this.options.chain_call_control.failed_number=0},importFromUserdirClicked:function(m){var g=$("#jstree_browser").jstree().get_selected(true);var l=this.modal.$el.find(".preserve-checkbox").is(":checked");var n=this.modal.$el.find(".link-checkbox").is(":checked");var h=this.select_extension.value();var o=this.select_genome.value();var j=g[0].type;var p=[];if(g.length<1){f.info("You must select some items first.")}else{this.modal.disableButton("Import");for(var k=g.length-1;k>=0;k--){if(g[k].li_attr.full_path!==undefined){p.push(g[k].li_attr.full_path)}}this.initChainCallControl({length:p.length,action:"adding_datasets"});if(j==="folder"){this.chainCallImportingFolders({paths:p,preserve_dirs:l,link_data:n,source:"userdir_folder",file_type:h,dbkey:o})}else{if(j==="file"){this.chainCallImportingUserdirFiles({paths:p,file_type:h,dbkey:o})}}}},fetchAndDisplayHistoryContents:function(i){var h=new d.HistoryContents({id:i});var g=this;h.fetch({success:function(k){var j=g.templateHistoryContents();g.histories.get(i).set({contents:k});g.modal.$el.find("#selected_history_content").html(j({history_contents:k.models.reverse()}))},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})},addAllDatasetsFromHistory:function(){var l=this.modal.$el.find("#selected_history_content").find(":checked");var g=[];var k=[];if(l.length<1){f.info("You must select some datasets first.")}else{this.modal.disableButton("Add");l.each(function(){var i=$(this.parentElement).data("id");if(i){g.push(i)}});for(var j=g.length-1;j>=0;j--){history_dataset_id=g[j];var h=new d.Item();h.url="/api/folders/"+this.options.id+"/contents";h.set({from_hda_id:history_dataset_id});k.push(h)}this.initChainCallControl({length:k.length,action:"adding_datasets"});this.chainCallAddingHdas(k)}},chainCallImportingIntoHistory:function(h,k){var g=this;var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets imported into history. Click this to start analysing it.","",{onclick:function(){window.location="/"}})}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be imported into history. Click this to see what was imported.","",{onclick:function(){window.location="/"}})}}}Galaxy.modal.hide();return true}var j=$.when(i.save({content:i.content,source:i.source}));j.done(function(){g.updateProgress();g.chainCallImportingIntoHistory(h,k)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallImportingIntoHistory(h,k)})},chainCallImportingUserdirFiles:function(g){var h=this;var i=g.paths.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected files imported into the current folder");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source=userdir_file&path="+i+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingUserdirFiles(g)}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingUserdirFiles(g)})},chainCallImportingFolders:function(g){var h=this;var i=g.paths.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected folders and their contents imported into the current folder.");Galaxy.modal.hide()}else{f.error("An error occured.")}return true}var j=$.when($.post("/api/libraries/datasets?encoded_folder_id="+h.id+"&source="+g.source+"&path="+i+"&preserve_dirs="+g.preserve_dirs+"&link_data="+g.link_data+"&file_type="+g.file_type+"&dbkey="+g.dbkey));j.done(function(k){h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})}).fail(function(){h.options.chain_call_control.failed_number+=1;h.updateProgress();h.chainCallImportingFolders({paths:g.paths,preserve_dirs:g.preserve_dirs,link_data:g.link_data,source:g.source,file_type:g.file_type,dbkey:g.dbkey})})},chainCallAddingHdas:function(h){var g=this;this.added_hdas=new d.Folder();var i=h.pop();if(typeof i=="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var j=$.when(i.save({from_hda_id:i.get("from_hda_id")}));j.done(function(k){Galaxy.libraries.folderListView.collection.add(k);g.updateProgress();g.chainCallAddingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallAddingHdas(h)})},chainCallDeletingHdas:function(h){var g=this;this.deleted_lddas=new d.Folder();var i=h.pop();if(typeof i==="undefined"){if(this.options.chain_call_control.failed_number===0){f.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){f.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){f.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var j=$.when(i.destroy());j.done(function(l){Galaxy.libraries.folderListView.collection.remove(i.id);g.updateProgress();if(Galaxy.libraries.folderListView.options.include_deleted){var k=new d.Item(l);Galaxy.libraries.folderListView.collection.add(k)}g.chainCallDeletingHdas(h)}).fail(function(){g.options.chain_call_control.failed_number+=1;g.updateProgress();g.chainCallDeletingHdas(h)})},checkIncludeDeleted:function(g){if(g.target.checked){Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var g=$("#folder_table").find(":checked");if(g.length===0){f.info("You must select at least one dataset for deletion.")}else{var k=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:k({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var h=[];g.each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});this.progressStep=100/h.length;this.progress=0;var m=[];for(var j=h.length-1;j>=0;j--){var l=new d.Item({id:h[j]});m.push(l)}this.options.chain_call_control.total_number=h.length;this.chainCallDeletingHdas(m)}},showLibInfo:function(){var h=Galaxy.libraries.folderListView.folderContainer.attributes.metadata.parent_library_id;var g=null;var i=this;if(Galaxy.libraries.libraryListView!==null){g=Galaxy.libraries.libraryListView.collection.get(h);this.showLibInfoModal(g)}else{g=new d.Library({id:h});g.fetch({success:function(){i.showLibInfoModal(g)},error:function(k,j){if(typeof j.responseJSON!=="undefined"){f.error(j.responseJSON.err_msg)}else{f.error("An error ocurred.")}}})}},showLibInfoModal:function(g){var h=this.templateLibInfoInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Library Information",body:h({library:g}),buttons:{Close:function(){Galaxy.modal.hide()}}})},showImportModal:function(g){switch(g.source){case"history":this.addFilesFromHistoryModal();break;case"importdir":break;case"path":this.importFilesFromPathModal();break;case"userdir":this.importFilesFromUserdirModal();break;default:Galaxy.libraries.library_router.back();f.error("Invalid import source.");break}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(" <span><strong>DATA LIBRARIES</strong></span>");tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" class="logged-dataset-manipulation" title="Include deleted datasets" style="display:none;"> | <input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"> include deleted | </input></span>');tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push("<% if(mutiple_add_dataset_options) { %>");tmpl_array.push(' <div class="btn-group add-library-items" style="display:none;">');tmpl_array.push(' <button title="Add Datasets to Current Folder" id="" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-plus"></span><span class="fa fa-file"></span><span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#folders/<%= id %>/import/history"> from History</a></li>');tmpl_array.push("<% if(user_library_import_dir !== null) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/userdir"> from User Directory</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li class="divider"></li>');tmpl_array.push(' <li class="dropdown-header">Admins only</li>');tmpl_array.push("<% if(allow_library_path_paste) { %>");tmpl_array.push(' <li><a href="#folders/<%= id %>/import/path">from Path</a></li>');tmpl_array.push("<% } %>");tmpl_array.push("<% } %>");tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push("<% } else { %>");tmpl_array.push(' <button style="display:none;" data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button add-library-items" type="button"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("<% } %>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button dataset-manipulation" style="margin-left: 0.5em; display:none;" type="button"><span class="fa fa-book"></span> to History</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group dataset-manipulation" style="margin-left: 0.5em; display:none; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> Download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button logged-dataset-manipulation" style="margin-left: 0.5em; display:none; " type="button"><span class="fa fa-times"></span> Delete</button>');tmpl_array.push(' <button data-id="<%- id %>" data-toggle="tooltip" data-placement="top" title="Show library information" id="toolbtn_show_libinfo" class="primary-button" style="margin-left: 0.5em;" type="button"><span class="fa fa-info-circle"></span> Library Info</button>');tmpl_array.push(' <span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki"><a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank"><button class="primary-button btn-xs" type="button"><span class="fa fa-question-circle"></span> Help</button></a></span>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateLibInfoInModal:function(){tmpl_array=[];tmpl_array.push('<div id="lif_info_modal">');tmpl_array.push("<h2>Library name:</h2>");tmpl_array.push('<p><%- library.get("name") %></p>');tmpl_array.push("<h3>Library description:</h3>");tmpl_array.push('<p><%- library.get("description") %></p>');tmpl_array.push("<h3>Library synopsis:</h3>");tmpl_array.push('<p><%- library.get("synopsis") %></p>');tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var g=[];g.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');g.push("Select history: ");g.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</span>");return _.template(g.join(""))},templateImportIntoHistoryProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateAddingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("Adding selected datasets to library folder <b><%= _.escape(folder_name) %></b>");g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateDeletingDatasetsProgressBar:function(){var g=[];g.push('<div class="import_text">');g.push("</div>");g.push('<div class="progress">');g.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');g.push(' <span class="completion_span">0% Complete</span>');g.push(" </div>");g.push("</div>");g.push("");return _.template(g.join(""))},templateBrowserModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-files-message">All files you select will be imported into the current folder.</div>');g.push('<div class="alert alert-info jstree-folders-message" style="display:none;">All files within the selected folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom:1em;">');g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting files" type="radio" name="jstree-radio" value="jstree-disable-folders" checked="checked"> Files');g.push("</label>");g.push('<label class="radio-inline">');g.push(' <input title="Switch to selecting folders" type="radio" name="jstree-radio" value="jstree-disable-files"> Folders');g.push("</label>");g.push("</div>");g.push('<div style="margin-bottom:1em;">');g.push('<label class="checkbox-inline jstree-preserve-structure" style="display:none;">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files" style="display:none;">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<div id="jstree_browser">');g.push("</div>");g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateImportPathModal:function(){var g=[];g.push('<div id="file_browser_modal">');g.push('<div class="alert alert-info jstree-folders-message">All files within the given folders and their subfolders will be imported into the current folder.</div>');g.push('<div style="margin-bottom: 0.5em;">');g.push('<label class="checkbox-inline jstree-preserve-structure">');g.push(' <input class="preserve-checkbox" type="checkbox" value="preserve_directory_structure">');g.push("Preserve directory structure");g.push(" </label>");g.push('<label class="checkbox-inline jstree-link-files">');g.push(' <input class="link-checkbox" type="checkbox" value="link_files">');g.push("Link files instead of copying");g.push(" </label>");g.push("</div>");g.push('<textarea id="import_paths" class="form-control" rows="5" placeholder="Absolute paths (or paths relative to Galaxy root) separated by newline"></textarea>');g.push("<hr />");g.push("<p>You can set extension type and genome for all imported datasets at once:</p>");g.push("<div>");g.push('Type: <span id="extension" class="extension" />');g.push(' Genome: <span id="genome" class="genome" />');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateAddFilesFromHistory:function(){var g=[];g.push('<div id="add_files_modal">');g.push('<div id="history_modal_combo_bulk">');g.push("Select history: ");g.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');g.push(" <% _.each(histories, function(history) { %>");g.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');g.push(" <% }); %>");g.push("</select>");g.push("</div>");g.push("<br/>");g.push('<div id="selected_history_content">');g.push("</div>");g.push("</div>");return _.template(g.join(""))},templateHistoryContents:function(){var g=[];g.push("<strong>Choose the datasets to import:</strong>");g.push("<ul>");g.push(" <% _.each(history_contents, function(history_item) { %>");g.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');g.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');g.push(" </li>");g.push(" <% }); %>");g.push("</ul>");return _.template(g.join(""))}});return{FolderToolbarView:b}}); \ No newline at end of file diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1232,7 +1232,8 @@ .select2-offscreen,.select2-offscreen:focus{clip:rect(0 0 0 0) !important;width:1px !important;height:1px !important;border:0 !important;margin:0 !important;padding:0 !important;overflow:hidden !important;position:absolute !important;outline:0 !important;left:0px !important;top:0px !important} .select2-display-none{display:none} .select2-measure-scrollbar{position:absolute;top:-10000px;left:-10000px;width:100px;height:100px;overflow:scroll} -@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} +@media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.select2-minwidth{min-width:256px} +.galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} .galaxy-frame .toggle{color:gold} .galaxy-frame .frame-background{z-index:1000;position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.6;background:#000;overflow:auto} .galaxy-frame .frame-shadow{z-index:1001;position:absolute;display:none;top:0px;left:0px;opacity:0.5;background:#2c3143;border:1px solid #888} diff -r 77af7639e78dbb57f66c1059789e8d652882459e -r 01f7ec31bc8161e7731c25df374495eac6425ba8 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -16,6 +16,10 @@ @import "select2.less"; + /* fix for zero width select2 - remove when fixed there */ +.select2-minwidth { + min-width: 256px; +} // galaxy sub-components @import "frame.less"; @import "upload.less"; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History panel: have all edit panels show contents in reverse order (not just current panel)
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb359ebefb58/ Changeset: eb359ebefb58 User: carlfeberhard Date: 2014-09-24 15:06:56+00:00 Summary: History panel: have all edit panels show contents in reverse order (not just current panel) Affected #: 9 files diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 client/galaxy/scripts/mvc/history/history-panel-edit-current.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js @@ -288,51 +288,23 @@ }, // ------------------------------------------------------------------------ sub-views - // reverse HID order - /** Override to reverse order of views - newest contents on top - * and add the current-content highlight class to currentContentId's view - */ + /** Override to add the current-content highlight class to currentContentId's view */ _attachItems : function( $whereTo ){ - var panel = this; - this.$list( $whereTo ).append( this.views.reverse().map( function( view ){ - // add current content - if( panel.currentContentId && view.model.id === panel.currentContentId ){ - panel.setCurrentContent( view ); - } - return view.$el; - })); + _super.prototype._attachItems.call( this, $whereTo ); + var panel = this, + currentContentView; + if( panel.currentContentId + && ( currentContentView = panel.viewFromModelId( panel.currentContentId ) ) ){ + panel.setCurrentContent( currentContentView ); + } return this; }, - /** Override to add datasets at the top */ + /** Override to remove any drill down panels */ addItemView : function( model, collection, options ){ - this.log( this + '.addItemView:', model ); - var panel = this; - if( !panel._filterItem( model ) ){ return undefined; } -//TODO: alternately, call collapse drilldown - // if this panel is currently hidden, return undefined - if( panel.panelStack.length ){ return this._collapseDrilldownPanel(); } - - var view = panel._createItemView( model ); - // use unshift and prepend to preserve reversed order - panel.views.unshift( view ); - - panel.scrollToTop(); - $({}).queue([ - function fadeOutEmptyMsg( next ){ - var $emptyMsg = panel.$emptyMessage(); - if( $emptyMsg.is( ':visible' ) ){ - $emptyMsg.fadeOut( panel.fxSpeed, next ); - } else { - next(); - } - }, - function createAndPrepend( next ){ - // render as hidden then slide down - panel.$list().prepend( view.render( 0 ).$el.hide() ); - view.$el.slideDown( panel.fxSpeed ); - } - ]); + var view = _super.prototype.addItemView.call( this, model, collection, options ); + if( !view ){ return view; } + if( this.panelStack.length ){ return this._collapseDrilldownPanel(); } return view; }, diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 client/galaxy/scripts/mvc/history/history-panel-edit.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js @@ -69,7 +69,7 @@ this.multiselectActions = attributes.multiselectActions || this._getActions(); }, - // ------------------------------------------------------------------------ panel rendering + // ------------------------------------------------------------------------ listeners /** listening for collection events */ _setUpCollectionListeners : function(){ _super.prototype._setUpCollectionListeners.call( this ); @@ -266,6 +266,25 @@ }, // ------------------------------------------------------------------------ sub-views + // reverse HID order + /** Override to reverse order of views - newest contents on top */ + _attachItems : function( $whereTo ){ + this.$list( $whereTo ).append( this.views.reverse().map( function( view ){ + return view.$el; + })); + return this; + }, + + /** Override to add new contents at the top */ + _attachView : function( view ){ + var panel = this; + // override to control where the view is added, how/whether it's rendered + panel.views.unshift( view ); + panel.$list().prepend( view.render( 0 ).$el.hide() ); + view.$el.slideDown( panel.fxSpeed ); + }, + + /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */ _getItemViewOptions : function( model ){ var options = _super.prototype._getItemViewOptions.call( this, model ); diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -402,6 +402,7 @@ /** Attach views in this.views to the model based on $whereTo */ _attachItems : function( $whereTo ){ + //ASSUMES: $list has been emptied this.$list( $whereTo ).append( this.views.map( function( view ){ return view.$el; })); @@ -436,23 +437,28 @@ var panel = this; if( !panel._filterItem( model ) ){ return undefined; } -//TODO: sorted? position? var view = panel._createItemView( model ); - panel.views.push( view ); - // hide the empty message if only view $( view ).queue( 'fx', [ + //TODO:? could poss. pubsub this function( next ){ panel.$emptyMessage().fadeOut( panel.fxSpeed, next ); }, function( next ){ -//TODO: auto render? -// slide down? - panel.$list().append( view.render().$el ); + panel._attachView( view ); next(); } ]); return view; }, + /** internal fn to add view (to both panel.views and panel.$list) */ + _attachView : function( view ){ + var panel = this; + // override to control where the view is added, how/whether it's rendered + panel.views.push( view ); + panel.$list().append( view.render( 0 ).$el.hide() ); + view.$el.slideDown( panel.fxSpeed ); + }, + /** Remove a view from the panel (if found) */ removeItemView : function( model, collection, options ){ this.log( this + '.removeItemView:', model ); diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -288,51 +288,23 @@ }, // ------------------------------------------------------------------------ sub-views - // reverse HID order - /** Override to reverse order of views - newest contents on top - * and add the current-content highlight class to currentContentId's view - */ + /** Override to add the current-content highlight class to currentContentId's view */ _attachItems : function( $whereTo ){ - var panel = this; - this.$list( $whereTo ).append( this.views.reverse().map( function( view ){ - // add current content - if( panel.currentContentId && view.model.id === panel.currentContentId ){ - panel.setCurrentContent( view ); - } - return view.$el; - })); + _super.prototype._attachItems.call( this, $whereTo ); + var panel = this, + currentContentView; + if( panel.currentContentId + && ( currentContentView = panel.viewFromModelId( panel.currentContentId ) ) ){ + panel.setCurrentContent( currentContentView ); + } return this; }, - /** Override to add datasets at the top */ + /** Override to remove any drill down panels */ addItemView : function( model, collection, options ){ - this.log( this + '.addItemView:', model ); - var panel = this; - if( !panel._filterItem( model ) ){ return undefined; } -//TODO: alternately, call collapse drilldown - // if this panel is currently hidden, return undefined - if( panel.panelStack.length ){ return this._collapseDrilldownPanel(); } - - var view = panel._createItemView( model ); - // use unshift and prepend to preserve reversed order - panel.views.unshift( view ); - - panel.scrollToTop(); - $({}).queue([ - function fadeOutEmptyMsg( next ){ - var $emptyMsg = panel.$emptyMessage(); - if( $emptyMsg.is( ':visible' ) ){ - $emptyMsg.fadeOut( panel.fxSpeed, next ); - } else { - next(); - } - }, - function createAndPrepend( next ){ - // render as hidden then slide down - panel.$list().prepend( view.render( 0 ).$el.hide() ); - view.$el.slideDown( panel.fxSpeed ); - } - ]); + var view = _super.prototype.addItemView.call( this, model, collection, options ); + if( !view ){ return view; } + if( this.panelStack.length ){ return this._collapseDrilldownPanel(); } return view; }, diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 static/scripts/mvc/history/history-panel-edit.js --- a/static/scripts/mvc/history/history-panel-edit.js +++ b/static/scripts/mvc/history/history-panel-edit.js @@ -69,7 +69,7 @@ this.multiselectActions = attributes.multiselectActions || this._getActions(); }, - // ------------------------------------------------------------------------ panel rendering + // ------------------------------------------------------------------------ listeners /** listening for collection events */ _setUpCollectionListeners : function(){ _super.prototype._setUpCollectionListeners.call( this ); @@ -266,6 +266,25 @@ }, // ------------------------------------------------------------------------ sub-views + // reverse HID order + /** Override to reverse order of views - newest contents on top */ + _attachItems : function( $whereTo ){ + this.$list( $whereTo ).append( this.views.reverse().map( function( view ){ + return view.$el; + })); + return this; + }, + + /** Override to add new contents at the top */ + _attachView : function( view ){ + var panel = this; + // override to control where the view is added, how/whether it's rendered + panel.views.unshift( view ); + panel.$list().prepend( view.render( 0 ).$el.hide() ); + view.$el.slideDown( panel.fxSpeed ); + }, + + /** In this override, add purgeAllowed and whether tags/annotation editors should be shown */ _getItemViewOptions : function( model ){ var options = _super.prototype._getItemViewOptions.call( this, model ); diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -402,6 +402,7 @@ /** Attach views in this.views to the model based on $whereTo */ _attachItems : function( $whereTo ){ + //ASSUMES: $list has been emptied this.$list( $whereTo ).append( this.views.map( function( view ){ return view.$el; })); @@ -436,23 +437,28 @@ var panel = this; if( !panel._filterItem( model ) ){ return undefined; } -//TODO: sorted? position? var view = panel._createItemView( model ); - panel.views.push( view ); - // hide the empty message if only view $( view ).queue( 'fx', [ + //TODO:? could poss. pubsub this function( next ){ panel.$emptyMessage().fadeOut( panel.fxSpeed, next ); }, function( next ){ -//TODO: auto render? -// slide down? - panel.$list().append( view.render().$el ); + panel._attachView( view ); next(); } ]); return view; }, + /** internal fn to add view (to both panel.views and panel.$list) */ + _attachView : function( view ){ + var panel = this; + // override to control where the view is added, how/whether it's rendered + panel.views.push( view ); + panel.$list().append( view.render( 0 ).$el.hide() ); + view.$el.slideDown( panel.fxSpeed ); + }, + /** Remove a view from the panel (if found) */ removeItemView : function( model, collection, options ){ this.log( this + '.removeItemView:', model ); diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 static/scripts/packed/mvc/history/history-panel-edit-current.js --- a/static/scripts/packed/mvc/history/history-panel-edit-current.js +++ b/static/scripts/packed/mvc/history/history-panel-edit-current.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){if(j.$el.is(":visible")){j.preferences.set("scrollPosition",$(this).scrollTop())}});this.on("new-model",function(){j.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){var j=this;this.$list(k).append(this.views.reverse().map(function(l){if(j.currentContentId&&l.model.id===j.currentContentId){j.setCurrentContent(l)}return l.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){if(j.$el.is(":visible")){j.preferences.set("scrollPosition",$(this).scrollTop())}});this.on("new-model",function(){j.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){g.prototype._attachItems.call(this,k);var j=this,l;if(j.currentContentId&&(l=j.viewFromModelId(j.currentContentId))){j.setCurrentContent(l)}return this},addItemView:function(l,m,k){var j=g.prototype.addItemView.call(this,l,m,k);if(!j){return j}if(this.panelStack.length){return this._collapseDrilldownPanel()}return j},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 static/scripts/packed/mvc/history/history-panel-edit.js --- a/static/scripts/packed/mvc/history/history-panel-edit.js +++ b/static/scripts/packed/mvc/history/history-panel-edit.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","utils/localization"],function(f,h,k,d,c,g,j,a,b){var i=f.HistoryPanel;var e=i.extend({HDAViewClass:c.HDAListItemEdit,HDCAViewClass:g.HDCAListItemEdit,initialize:function(l){l=l||{};i.prototype.initialize.call(this,l);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=l.purgeAllowed||false;this.annotationEditorShown=l.annotationEditorShown||false;this.tagsEditorShown=l.tagsEditorShown||false;this.multiselectActions=l.multiselectActions||this._getActions()},_setUpCollectionListeners:function(){i.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(l){this.model.fetch()},this);return this},_setUpModelListeners:function(){i.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var l=i.prototype._buildNewRender.call(this);if(!this.model){return l}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(l);this._renderAnnotation(l)}return l},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(l.find(".controls .actions"))})},_renderAnnotation:function(l){var m=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:l.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDAAnnotationEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDAAnnotationEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(l.find(".controls .actions"))})},_setUpBehaviors:function(l){l=l||this.$el;i.prototype._setUpBehaviors.call(this,l);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new PopupMenu(l.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var m=this,n=".controls .name";l.find(n).attr("title",b("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(o){var p=m.model.get("name");if(o&&o!==p){m.$el.find(n).text(o);m.model.save({name:o}).fail(function(){m.$el.find(n).text(m.model.previous("name"))})}else{m.$el.find(n).text(p)}}})},_getActions:function(){var l=this,m=[{html:b("Hide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.hide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Unhide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.unhide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Delete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype["delete"];l.getSelectedModels().ajaxQueue(n)}},{html:b("Undelete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.undelete;l.getSelectedModels().ajaxQueue(n)}}];if(l.purgeAllowed){m.push({html:b("Permanently delete datasets"),func:function(){if(confirm(b("This will permanently remove the data in your datasets. Are you sure?"))){var n=d.HistoryDatasetAssociation.prototype.purge;l.getSelectedModels().ajaxQueue(n)}}})}m.push({html:b("Build Dataset List"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"list")}});m.push({html:b("Build Dataset Pair"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"paired")}});m.push({html:b("Build List of Dataset Pairs"),func:_.bind(l._showPairedCollectionModal,l)});return m},_showPairedCollectionModal:function(){var l=this,m=l.getSelectedModels().toJSON().filter(function(n){return n.history_content_type==="dataset"&&n.state===k.OK});if(m.length){require(["mvc/collection/paired-collection-creator"],function(n){window.creator=n.pairedCollectionCreatorModal(m,{historyId:l.model.id})})}else{}},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){if(l.get("deleted")&&!this.storage.get("show_deleted")){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){if(l.hidden()&&!this.storage.get("show_hidden")){this.removeItemView(l)}},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:e}}); \ No newline at end of file +define(["mvc/history/history-panel","mvc/history/history-contents","mvc/dataset/states","mvc/history/hda-model","mvc/history/hda-li-edit","mvc/history/hdca-li-edit","mvc/tags","mvc/annotations","utils/localization"],function(f,h,k,d,c,g,j,a,b){var i=f.HistoryPanel;var e=i.extend({HDAViewClass:c.HDAListItemEdit,HDCAViewClass:g.HDCAListItemEdit,initialize:function(l){l=l||{};i.prototype.initialize.call(this,l);this.tagsEditor=null;this.annotationEditor=null;this.purgeAllowed=l.purgeAllowed||false;this.annotationEditorShown=l.annotationEditorShown||false;this.tagsEditorShown=l.tagsEditorShown||false;this.multiselectActions=l.multiselectActions||this._getActions()},_setUpCollectionListeners:function(){i.prototype._setUpCollectionListeners.call(this);this.collection.on("change:deleted",this._handleHdaDeletionChange,this);this.collection.on("change:visible",this._handleHdaVisibleChange,this);this.collection.on("change:purged",function(l){this.model.fetch()},this);return this},_setUpModelListeners:function(){i.prototype._setUpModelListeners.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);return this},_buildNewRender:function(){var l=i.prototype._buildNewRender.call(this);if(!this.model){return l}if(Galaxy&&Galaxy.currUser&&Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(l);this._renderAnnotation(l)}return l},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(l.find(".controls .actions"))})},_renderAnnotation:function(l){var m=this;this.annotationEditor=new a.AnnotationEditor({model:this.model,el:l.find(".controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDAAnnotationEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDAAnnotationEditors(false,m.fxSpeed)},$activator:faIconButton({title:b("Edit history annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(l.find(".controls .actions"))})},_setUpBehaviors:function(l){l=l||this.$el;i.prototype._setUpBehaviors.call(this,l);if(!this.model){return}if(this.multiselectActions.length){this.actionsPopup=new PopupMenu(l.find(".list-action-popup-btn"),this.multiselectActions)}if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var m=this,n=".controls .name";l.find(n).attr("title",b("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(o){var p=m.model.get("name");if(o&&o!==p){m.$el.find(n).text(o);m.model.save({name:o}).fail(function(){m.$el.find(n).text(m.model.previous("name"))})}else{m.$el.find(n).text(p)}}})},_getActions:function(){var l=this,m=[{html:b("Hide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.hide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Unhide datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.unhide;l.getSelectedModels().ajaxQueue(n)}},{html:b("Delete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype["delete"];l.getSelectedModels().ajaxQueue(n)}},{html:b("Undelete datasets"),func:function(){var n=d.HistoryDatasetAssociation.prototype.undelete;l.getSelectedModels().ajaxQueue(n)}}];if(l.purgeAllowed){m.push({html:b("Permanently delete datasets"),func:function(){if(confirm(b("This will permanently remove the data in your datasets. Are you sure?"))){var n=d.HistoryDatasetAssociation.prototype.purge;l.getSelectedModels().ajaxQueue(n)}}})}m.push({html:b("Build Dataset List"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"list")}});m.push({html:b("Build Dataset Pair"),func:function(){l.getSelectedModels().promoteToHistoryDatasetCollection(l.model,"paired")}});m.push({html:b("Build List of Dataset Pairs"),func:_.bind(l._showPairedCollectionModal,l)});return m},_showPairedCollectionModal:function(){var l=this,m=l.getSelectedModels().toJSON().filter(function(n){return n.history_content_type==="dataset"&&n.state===k.OK});if(m.length){require(["mvc/collection/paired-collection-creator"],function(n){window.creator=n.pairedCollectionCreatorModal(m,{historyId:l.model.id})})}else{}},_attachItems:function(l){this.$list(l).append(this.views.reverse().map(function(m){return m.$el}));return this},_attachView:function(m){var l=this;l.views.unshift(m);l.$list().prepend(m.render(0).$el.hide());m.$el.slideDown(l.fxSpeed)},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){if(l.get("deleted")&&!this.storage.get("show_deleted")){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){if(l.hidden()&&!this.storage.get("show_hidden")){this.removeItemView(l)}},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit:e}}); \ No newline at end of file diff -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 -r eb359ebefb58d6b80ab5af14db05843168c428a8 static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){var h=this.model?this.model.get("id"):null;this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(h&&g.get("id")!==h){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g._attachView(f);k()}]);return f},_attachView:function(g){var f=this;f.views.push(g);f.$list().append(g.render(0).$el.hide());g.$el.slideDown(f.fxSpeed)},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){var h=this.model?this.model.get("id"):null;this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(h&&g.get("id")!==h){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Better stderr and exit code handling for interal wig-to-bigwig converter.
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/77af7639e78d/ Changeset: 77af7639e78d Branch: next-stable User: jgoecks Date: 2014-09-24 14:24:50+00:00 Summary: Better stderr and exit code handling for interal wig-to-bigwig converter. Affected #: 1 file diff -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b -r 77af7639e78dbb57f66c1059789e8d652882459e lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml --- a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml +++ b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml @@ -3,7 +3,10 @@ <requirements><requirement type="package">ucsc_tools</requirement></requirements> - <command>grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output</command> + <command> + grep -v "^track" $input | wigToBigWig -clip stdin $chromInfo $output + 2>&1 || echo "Error running wiggle to bigwig converter." >&2 + </command><inputs><page><param format="wig" name="input" type="data" label="Choose wiggle"/> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 24 Sep '14

24 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/30a9650534c3/ Changeset: 30a9650534c3 Branch: next-stable User: carlfeberhard Date: 2014-09-24 13:49:41+00:00 Summary: Fixes to current dataset indicator and focused icon buttons Affected #: 11 files diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b client/galaxy/scripts/mvc/history/history-panel-edit-current.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js @@ -87,8 +87,17 @@ _super.prototype._setUpListeners.call( this ); var panel = this; + // cache the scroll position (only if visible) this.$scrollContainer().on( 'scroll', function( ev ){ - panel.preferences.set( 'scrollPosition', $( this ).scrollTop() ); + if( panel.$el.is( ':visible' ) ){ + panel.preferences.set( 'scrollPosition', $( this ).scrollTop() ); + } + }); + + //TODO: doesn't work + // reset scroll position when there's a new history + this.on( 'new-model', function(){ + panel.preferences.set( 'scrollPosition', 0 ); }); }, @@ -267,7 +276,6 @@ _swapNewRender : function( $newRender ){ _super.prototype._swapNewRender.call( this, $newRender ); var panel = this; - _.delay( function(){ var pos = panel.preferences.get( 'scrollPosition' ); if( pos ){ @@ -289,7 +297,7 @@ this.$list( $whereTo ).append( this.views.reverse().map( function( view ){ // add current content if( panel.currentContentId && view.model.id === panel.currentContentId ){ - view.$el.addClass( 'current-content' ); + panel.setCurrentContent( view ); } return view.$el; })); diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -798,6 +798,8 @@ this.freeViews(); if( model ){ + var oldModelId = this.model? this.model.get( 'id' ): null; + // set up the new model with user, logger, storage, events this.model = model; if( this.logger ){ @@ -814,7 +816,9 @@ ( attributes.collection || ( new this.collectionClass([]) ) ); this._setUpCollectionListeners(); - this.trigger( 'new-model', this ); + if( oldModelId && model.get( 'id' ) !== oldModelId ){ + this.trigger( 'new-model', this ); + } } return this; }, diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -87,8 +87,17 @@ _super.prototype._setUpListeners.call( this ); var panel = this; + // cache the scroll position (only if visible) this.$scrollContainer().on( 'scroll', function( ev ){ - panel.preferences.set( 'scrollPosition', $( this ).scrollTop() ); + if( panel.$el.is( ':visible' ) ){ + panel.preferences.set( 'scrollPosition', $( this ).scrollTop() ); + } + }); + + //TODO: doesn't work + // reset scroll position when there's a new history + this.on( 'new-model', function(){ + panel.preferences.set( 'scrollPosition', 0 ); }); }, @@ -267,7 +276,6 @@ _swapNewRender : function( $newRender ){ _super.prototype._swapNewRender.call( this, $newRender ); var panel = this; - _.delay( function(){ var pos = panel.preferences.get( 'scrollPosition' ); if( pos ){ @@ -289,7 +297,7 @@ this.$list( $whereTo ).append( this.views.reverse().map( function( view ){ // add current content if( panel.currentContentId && view.model.id === panel.currentContentId ){ - view.$el.addClass( 'current-content' ); + panel.setCurrentContent( view ); } return view.$el; })); diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -798,6 +798,8 @@ this.freeViews(); if( model ){ + var oldModelId = this.model? this.model.get( 'id' ): null; + // set up the new model with user, logger, storage, events this.model = model; if( this.logger ){ @@ -814,7 +816,9 @@ ( attributes.collection || ( new this.collectionClass([]) ) ); this._setUpCollectionListeners(); - this.trigger( 'new-model', this ); + if( oldModelId && model.get( 'id' ) !== oldModelId ){ + this.trigger( 'new-model', this ); + } } return this; }, diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/scripts/packed/mvc/history/history-panel-edit-current.js --- a/static/scripts/packed/mvc/history/history-panel-edit-current.js +++ b/static/scripts/packed/mvc/history/history-panel-edit-current.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){j.preferences.set("scrollPosition",$(this).scrollTop())})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){var j=this;this.$list(k).append(this.views.reverse().map(function(l){if(j.currentContentId&&l.model.id===j.currentContentId){l.$el.addClass("current-content")}return l.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){if(j.$el.is(":visible")){j.preferences.set("scrollPosition",$(this).scrollTop())}});this.on("new-model",function(){j.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){var j=this;this.$list(k).append(this.views.reverse().map(function(l){if(j.currentContentId&&l.model.id===j.currentContentId){j.setCurrentContent(l)}return l.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){var h=this.model?this.model.get("id"):null;this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(h&&g.get("id")!==h){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1833,8 +1833,7 @@ .icon-button.link{background:url(../images/silk/link.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px} .icon-button.link-broken{background:url(../images/silk/link_break.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px} .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px} -.icon-btn,.ui-button-icon,.ui-button-icon-plain{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;border-radius:3px;border:1px solid #bfbfbf;background-color:#f2f2f2;color:#333;cursor:pointer} -.icon-btn:hover{background-color:white;color:maroon} +.icon-btn,.ui-button-icon,.ui-button-icon-plain{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;border-radius:3px;border:1px solid #bfbfbf;background-color:#f2f2f2;color:#333;cursor:pointer}.icon-btn:focus,.icon-btn:hover{outline:0;background-color:white;color:maroon} .icon-btn.disabled{background-color:transparent;color:#BBB;border-color:#BBB} .icon-btn-group{display:inline-block}.icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} @@ -1968,7 +1967,8 @@ .annotated-history-panel table.list-items>tbody>tr>td:nth-child(2){padding:8px 16px 8px 16px;white-space:pre-wrap} .annotated-history-panel table.list-items>tbody>tr>td>.list-item{border:0px} .annotated-history-panel .empty-message{margin-top:8px} -.current-history-panel .list-item.history-content.current-content{border:2px solid black;border-bottom-width:2px}.current-history-panel .list-item.history-content.current-content .title-bar{padding:5px 8px 6px 6px} +.current-history-panel .list-item.history-content.current-content{border:2px solid #333;border-bottom-width:2px}.current-history-panel .list-item.history-content.current-content .primary-actions{margin:5px 8px 0px 0px} +.current-history-panel .list-item.history-content.current-content .title-bar{padding:5px 8px 5px 6px} .current-history-panel .list-item.history-content.current-content .details{padding:0px 8px 5px 6px} body.historyPage{background:#dfe5f9;color:#000;margin:5px;border:0;padding:0} div.historyLinks{margin:5px 5px} diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -455,16 +455,14 @@ -.quota-meter-container -{ +.quota-meter-container { position: absolute; top: 0; right: 0; height: 32px; } -.quota-meter -{ +.quota-meter { position: absolute; top: 8px; right: 8px; @@ -473,8 +471,7 @@ background-color: @progress-bg; } -.quota-meter-bar -{ +.quota-meter-bar { position: absolute; top: 0; left: 0; @@ -482,18 +479,15 @@ background-color: @brand-primary; } -.quota-meter-bar-warn -{ +.quota-meter-bar-warn { background-color: @brand-warning; } -.quota-meter-bar-error -{ +.quota-meter-bar-error { background-color: @brand-danger; } -.quota-meter-text -{ +.quota-meter-text { position: absolute; top: 50%; left: 0; diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -590,25 +590,14 @@ // ---------------------------------------------------------------------------- current-history-panel .current-history-panel { .list-item.history-content.current-content { - //border-top: 2px solid black; - //border-right: 1px solid black; - //border-bottom: 2px solid black; - //border-left: 1px solid black; - //.title-bar { - // border-color: black; - // background: black; - // color: white; - //} - - //position: relative; - //margin-left: -24px; - //z-index: 1000; - - border: 2px solid black; + border: 2px solid #333; border-bottom-width: 2px; + .primary-actions { + margin: 5px 8px 0px 0px; + } .title-bar { - padding: 5px 8px 6px 6px; + padding: 5px 8px 5px 6px; } .details { padding: 0px 8px 5px 6px; diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/style/src/less/list-item.less --- a/static/style/src/less/list-item.less +++ b/static/style/src/less/list-item.less @@ -73,6 +73,10 @@ word-break: break-all; line-height: 16px; } +//TODO: show keyboard/tab focus for keyboard users + //&:focus { + // color: maroon; + //} } .primary-actions { diff -r 803755d0cd2098165c819c44b81f7f2591f9c69e -r 30a9650534c3e3743b6303bb2f9326c55ec4c55b static/style/src/less/ui/icon-btn.less --- a/static/style/src/less/ui/icon-btn.less +++ b/static/style/src/less/ui/icon-btn.less @@ -44,16 +44,13 @@ cursor: pointer; - // tweaks - //TODO: not working - span - //.fa-comment { - // display: inline-block; - // margin-bottom: 4px; - //} -} -.icon-btn:hover { - background-color: white; - color: maroon; + &:focus, + &:hover { + outline: 0; + background-color: white; + color: maroon; + } + } .icon-btn.disabled { background-color: transparent; https://bitbucket.org/galaxy/galaxy-central/commits/6b5dcb4c1918/ Changeset: 6b5dcb4c1918 User: carlfeberhard Date: 2014-09-24 13:50:01+00:00 Summary: Merge default Affected #: 11 files diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 client/galaxy/scripts/mvc/history/history-panel-edit-current.js --- a/client/galaxy/scripts/mvc/history/history-panel-edit-current.js +++ b/client/galaxy/scripts/mvc/history/history-panel-edit-current.js @@ -87,8 +87,17 @@ _super.prototype._setUpListeners.call( this ); var panel = this; + // cache the scroll position (only if visible) this.$scrollContainer().on( 'scroll', function( ev ){ - panel.preferences.set( 'scrollPosition', $( this ).scrollTop() ); + if( panel.$el.is( ':visible' ) ){ + panel.preferences.set( 'scrollPosition', $( this ).scrollTop() ); + } + }); + + //TODO: doesn't work + // reset scroll position when there's a new history + this.on( 'new-model', function(){ + panel.preferences.set( 'scrollPosition', 0 ); }); }, @@ -267,7 +276,6 @@ _swapNewRender : function( $newRender ){ _super.prototype._swapNewRender.call( this, $newRender ); var panel = this; - _.delay( function(){ var pos = panel.preferences.get( 'scrollPosition' ); if( pos ){ @@ -289,7 +297,7 @@ this.$list( $whereTo ).append( this.views.reverse().map( function( view ){ // add current content if( panel.currentContentId && view.model.id === panel.currentContentId ){ - view.$el.addClass( 'current-content' ); + panel.setCurrentContent( view ); } return view.$el; })); diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 client/galaxy/scripts/mvc/list/list-panel.js --- a/client/galaxy/scripts/mvc/list/list-panel.js +++ b/client/galaxy/scripts/mvc/list/list-panel.js @@ -798,6 +798,8 @@ this.freeViews(); if( model ){ + var oldModelId = this.model? this.model.get( 'id' ): null; + // set up the new model with user, logger, storage, events this.model = model; if( this.logger ){ @@ -814,7 +816,9 @@ ( attributes.collection || ( new this.collectionClass([]) ) ); this._setUpCollectionListeners(); - this.trigger( 'new-model', this ); + if( oldModelId && model.get( 'id' ) !== oldModelId ){ + this.trigger( 'new-model', this ); + } } return this; }, diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/scripts/mvc/history/history-panel-edit-current.js --- a/static/scripts/mvc/history/history-panel-edit-current.js +++ b/static/scripts/mvc/history/history-panel-edit-current.js @@ -87,8 +87,17 @@ _super.prototype._setUpListeners.call( this ); var panel = this; + // cache the scroll position (only if visible) this.$scrollContainer().on( 'scroll', function( ev ){ - panel.preferences.set( 'scrollPosition', $( this ).scrollTop() ); + if( panel.$el.is( ':visible' ) ){ + panel.preferences.set( 'scrollPosition', $( this ).scrollTop() ); + } + }); + + //TODO: doesn't work + // reset scroll position when there's a new history + this.on( 'new-model', function(){ + panel.preferences.set( 'scrollPosition', 0 ); }); }, @@ -267,7 +276,6 @@ _swapNewRender : function( $newRender ){ _super.prototype._swapNewRender.call( this, $newRender ); var panel = this; - _.delay( function(){ var pos = panel.preferences.get( 'scrollPosition' ); if( pos ){ @@ -289,7 +297,7 @@ this.$list( $whereTo ).append( this.views.reverse().map( function( view ){ // add current content if( panel.currentContentId && view.model.id === panel.currentContentId ){ - view.$el.addClass( 'current-content' ); + panel.setCurrentContent( view ); } return view.$el; })); diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/scripts/mvc/list/list-panel.js --- a/static/scripts/mvc/list/list-panel.js +++ b/static/scripts/mvc/list/list-panel.js @@ -798,6 +798,8 @@ this.freeViews(); if( model ){ + var oldModelId = this.model? this.model.get( 'id' ): null; + // set up the new model with user, logger, storage, events this.model = model; if( this.logger ){ @@ -814,7 +816,9 @@ ( attributes.collection || ( new this.collectionClass([]) ) ); this._setUpCollectionListeners(); - this.trigger( 'new-model', this ); + if( oldModelId && model.get( 'id' ) !== oldModelId ){ + this.trigger( 'new-model', this ); + } } return this; }, diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/scripts/packed/mvc/history/history-panel-edit-current.js --- a/static/scripts/packed/mvc/history/history-panel-edit-current.js +++ b/static/scripts/packed/mvc/history/history-panel-edit-current.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){j.preferences.set("scrollPosition",$(this).scrollTop())})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){var j=this;this.$list(k).append(this.views.reverse().map(function(l){if(j.currentContentId&&l.model.id===j.currentContentId){l.$el.addClass("current-content")}return l.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/history/history-panel-edit","mvc/collection/collection-panel","mvc/base-mvc","utils/localization"],function(d,c,a,h,b){var e=h.SessionStorageModel.extend({defaults:{tagsEditorShown:false,annotationEditorShown:false,scrollPosition:0},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});e.storageKey=function f(){return("history-panel")};var g=c.HistoryPanelEdit;var i=g.extend({className:g.prototype.className+" current-history-panel",emptyMsg:b("This history is empty. Click 'Get Data' on the left tool menu to start"),noneFoundMsg:b("No matching datasets found"),HDCAViewClass:g.prototype.HDCAViewClass.extend({foldoutStyle:"drilldown"}),initialize:function(j){j=j||{};this.preferences=new e(_.extend({id:e.storageKey()},_.pick(j,_.keys(e.prototype.defaults))));g.prototype.initialize.call(this,j);this.panelStack=[];this.currentContentId=j.currentContentId||null},_setUpListeners:function(){g.prototype._setUpListeners.call(this);var j=this;this.$scrollContainer().on("scroll",function(k){if(j.$el.is(":visible")){j.preferences.set("scrollPosition",$(this).scrollTop())}});this.on("new-model",function(){j.preferences.set("scrollPosition",0)})},loadCurrentHistory:function(k){this.debug(this+".loadCurrentHistory");var j=this;return this.loadHistoryWithDetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/set_as_current?id="+m)};return this.loadHistoryWithDetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",b("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.getJSON(galaxy_config.root+"history/create_new_current")};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},setModel:function(k,j,l){g.prototype.setModel.call(this,k,j,l);if(this.model){this.log("checking for updates");this.model.checkForUpdates()}return this},_setUpCollectionListeners:function(){g.prototype._setUpCollectionListeners.call(this);this.collection.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeItemView(this.viewFromModel(k))}},this)},_setUpModelListeners:function(){g.prototype._setUpModelListeners.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}},_buildNewRender:function(){if(!this.model){return $()}var j=g.prototype._buildNewRender.call(this);j.find(".search").prependTo(j.find(".controls"));this._renderQuotaMessage(j);return j},_renderQuotaMessage:function(j){j=j||this.$el;return $(this.templates.quotaMsg({},this)).prependTo(j.find(".messages"))},_renderEmptyMessage:function(l){var k=this,j=k.$emptyMessage(l),m=$(".toolMenuContainer");if((_.isEmpty(k.views)&&!k.searchFor)&&(Galaxy&&Galaxy.upload&&m.size())){j.empty();j.html([b("This history is empty"),". ",b("You can "),'<a class="uploader-link" href="javascript:void(0)">',b("load your own data"),"</a>",b(" or "),'<a class="get-data-link" href="javascript:void(0)">',b("get data from an external source"),"</a>"].join(""));j.find(".uploader-link").click(function(n){Galaxy.upload._eventShow(n)});j.find(".get-data-link").click(function(n){m.parent().scrollTop(0);m.find('span:contains("Get Data")').click()});return j.show()}return g.prototype._renderEmptyMessage.call(this,l)},_renderTags:function(j){var k=this;g.prototype._renderTags.call(this,j);if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}this.tagsEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("tagsEditorShown",l.hidden)})},_renderAnnotation:function(j){var k=this;g.prototype._renderAnnotation.call(this,j);if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}this.annotationEditor.on("hiddenUntilActivated:shown hiddenUntilActivated:hidden",function(l){k.preferences.set("annotationEditorShown",l.hidden)})},_swapNewRender:function(k){g.prototype._swapNewRender.call(this,k);var j=this;_.delay(function(){var l=j.preferences.get("scrollPosition");if(l){j.scrollTo(l)}},10);return this},_attachItems:function(k){var j=this;this.$list(k).append(this.views.reverse().map(function(l){if(j.currentContentId&&l.model.id===j.currentContentId){j.setCurrentContent(l)}return l.$el}));return this},addItemView:function(o,p,n){this.log(this+".addItemView:",o);var l=this;if(!l._filterItem(o)){return undefined}if(l.panelStack.length){return this._collapseDrilldownPanel()}var k=l._createItemView(o);l.views.unshift(k);l.scrollToTop();$({}).queue([function m(r){var q=l.$emptyMessage();if(q.is(":visible")){q.fadeOut(l.fxSpeed,r)}else{r()}},function j(q){l.$list().prepend(k.render(0).$el.hide());k.$el.slideDown(l.fxSpeed)}]);return k},_setUpItemViewListeners:function(k){var j=this;g.prototype._setUpItemViewListeners.call(j,k);k.on("expanded:drilldown",function(m,l){this._expandDrilldownPanel(l)},this);k.on("collapsed:drilldown",function(m,l){this._collapseDrilldownPanel(l)},this);k.on("display edit params rerun report-err visualize",function(l,m){this.setCurrentContent(l)},this);return this},setCurrentContent:function(j){this.$(".history-content.current-content").removeClass("current-content");if(j){j.$el.addClass("current-content");this.currentContentId=j.model.id}else{this.currentContentId=null}},_expandDrilldownPanel:function(j){this.panelStack.push(j);this.$("> .controls").add(this.$list()).hide();j.parentName=this.model.get("name");this.$el.append(j.render().$el)},_collapseDrilldownPanel:function(j){this.panelStack.pop();this.render()},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(b("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(b("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});i.prototype.templates=(function(){var j=h.wrapTemplate(['<div class="quota-message errormessage">',b("You are over your disk quota"),". ",b("Tool execution is on hold until your disk usage drops below your allocated quota"),".","</div>"],"history");return _.extend(_.clone(g.prototype.templates),{quotaMsg:j})}());return{CurrentHistoryPanel:i}}); \ No newline at end of file diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/scripts/packed/mvc/list/list-panel.js --- a/static/scripts/packed/mvc/list/list-panel.js +++ b/static/scripts/packed/mvc/list/list-panel.js @@ -1,1 +1,1 @@ -define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();this.trigger("new-model",this)}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file +define(["mvc/list/list-item","mvc/base-mvc","utils/localization"],function(d,b,c){var e=Backbone.View.extend(b.LoggableMixin).extend({viewClass:d.ListItemView,collectionClass:Backbone.Collection,tagName:"div",className:"list-panel",fxSpeed:"fast",emptyMsg:c("This list is empty"),noneFoundMsg:c("No matching items found"),searchPlaceholder:c("search"),multiselectActions:[],initialize:function(f,g){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.filters=[];this.searchFor=f.searchFor||"";this.indicator=new LoadingIndicator(this.$el);this.selecting=(f.selecting!==undefined)?f.selecting:true;this.selected=f.selected||[];this.lastSelected=null;this.viewClass=f.viewClass||this.viewClass;this.views=[];this.collection=f.collection||(new this.collectionClass([]));this.filters=f.filters||[];this.$scrollContainer=f.$scrollContainer||this.$scrollContainer;this.title=f.title||"";this.subtitle=f.subtitle||"";this.multiselectActions=f.multiselectActions||this.multiselectActions;this.actionsPopup=null;this._setUpListeners()},freeViews:function(){_.each(this.views,function(f){f.off()});this.views=[];return this},_setUpListeners:function(){this.off();this.on("error",function(g,j,f,i,h){console.error(g,j,f,i,h)},this);this.on("loading",function(){this._showLoadingIndicator("loading...",40)},this);this.on("loading-done",function(){this._hideLoadingIndicator(40)},this);this.once("rendered",function(){this.trigger("rendered:initial",this)},this);if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}this._setUpCollectionListeners();this._setUpViewListeners();return this},_setUpCollectionListeners:function(){this.log(this+"._setUpCollectionListeners",this.collection);this.collection.off();this.collection.on("error",function(g,j,f,i,h){this.trigger("error",g,j,f,i,h)},this);this.collection.on("reset",function(){this.renderItems()},this);this.collection.on("add",this.addItemView,this);this.collection.on("remove",this.removeItemView,this);if(this.logger){this.collection.on("all",function(f){this.info(this+"(collection)",arguments)},this)}return this},_setUpViewListeners:function(){this.log(this+"._setUpViewListeners");this.on("view:selected",function(f,g){if(g&&g.shiftKey&&this.lastSelected){var h=this.viewFromModelId(this.lastSelected);if(h){this.selectRange(f,h)}}this.selected.push(f.model.id);this.lastSelected=f.model.id},this);this.on("view:de-selected",function(f,g){this.selected=_.without(this.selected,f.model.id)},this)},render:function(g){this.log(this+".render",g);var f=this._buildNewRender();this._setUpBehaviors(f);this._queueNewRender(f,g);return this},_buildNewRender:function(){this.debug(this+"(ListPanel)._buildNewRender");var f=$(this.templates.el({},this));this._renderControls(f);this._renderTitle(f);this._renderSubtitle(f);this._renderSearch(f);this.renderItems(f);return f},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var f=$(this.templates.controls({},this));g.find(".controls").replaceWith(f);return f},_renderTitle:function(f){},_renderSubtitle:function(f){},_queueNewRender:function(g,h){h=(h===undefined)?(this.fxSpeed):(h);var f=this;f.log("_queueNewRender:",g,h);$(f).queue("fx",[function(i){this.$el.fadeOut(h,i)},function(i){f._swapNewRender(g);i()},function(i){this.$el.fadeIn(h,i)},function(i){f.trigger("rendered",f);i()}])},_swapNewRender:function(f){this.$el.empty().attr("class",this.className).append(f.children());if(this.selecting){this.showSelectors(0)}return this},_setUpBehaviors:function(f){f=f||this.$el;f.find(".controls [title]").tooltip({placement:"bottom"});return this},$scrollContainer:function(){return this.$el.parent().parent()},$list:function(f){return(f||this.$el).find("> .list-items")},$messages:function(f){return(f||this.$el).find("> .controls .messages")},$emptyMessage:function(f){return(f||this.$el).find("> .empty-message")},renderItems:function(h){h=h||this.$el;var f=this;f.log(this+".renderItems",h);var g=f.$list(h);f.views=f._filterCollection().map(function(i){return f._createItemView(i).render(0)});g.empty();if(f.views.length){f._attachItems(h);f.$emptyMessage(h).hide()}else{f._renderEmptyMessage(h).show()}return f.views},_filterCollection:function(){var f=this;return f.collection.filter(_.bind(f._filterItem,f))},_filterItem:function(g){var f=this;return(_.every(f.filters.map(function(h){return h.call(g)})))&&(!f.searchFor||g.matchesAll(f.searchFor))},_createItemView:function(h){var i=this._getItemViewClass(h),g=_.extend(this._getItemViewOptions(h),{model:h}),f=new i(g);this._setUpItemViewListeners(f);return f},_getItemViewClass:function(f){return this.viewClass},_getItemViewOptions:function(f){return{fxSpeed:this.fxSpeed,expanded:false,selectable:this.selecting,selected:_.contains(this.selected,f.id),draggable:this.dragging}},_setUpItemViewListeners:function(g){var f=this;g.on("all",function(){var h=Array.prototype.slice.call(arguments,0);h[0]="view:"+h[0];f.trigger.apply(f,h)});return f},_attachItems:function(f){this.$list(f).append(this.views.map(function(g){return g.$el}));return this},_renderEmptyMessage:function(f){this.debug("_renderEmptyMessage",f,this.searchFor);var g=this.searchFor?this.noneFoundMsg:this.emptyMsg;return this.$emptyMessage(f).text(g)},expandAll:function(){_.each(this.views,function(f){f.expand()})},collapseAll:function(){_.each(this.views,function(f){f.collapse()})},addItemView:function(i,j,h){this.log(this+".addItemView:",i);var g=this;if(!g._filterItem(i)){return undefined}var f=g._createItemView(i);g.views.push(f);$(f).queue("fx",[function(k){g.$emptyMessage().fadeOut(g.fxSpeed,k)},function(k){g.$list().append(f.render().$el);k()}]);return f},removeItemView:function(i,j,h){this.log(this+".removeItemView:",i);var g=this,f=g.viewFromModel(i);if(!f){return undefined}$({}).queue("fx",[function(k){f.$el.fadeOut(g.fxSpeed,k)},function(k){g.views=_.without(g.views,f);f.remove();if(!g.views.length){g._renderEmptyMessage().fadeIn(g.fxSpeed,k)}else{k()}}]);return f},viewFromModelId:function(g){for(var f=0;f<this.views.length;f++){if(this.views[f].model.id===g){return this.views[f]}}return undefined},viewFromModel:function(f){return this.viewFromModelId(f.id)},viewsWhereModel:function(f){return this.views.filter(function(g){var i=g.model.toJSON();for(var h in f){if(f.hasOwnProperty(h)){if(i[h]!==g.model.get(h)){return false}}}return true})},viewRange:function(i,h){if(i===h){return(i)?([i]):([])}var g=this.views.indexOf(i),f=this.views.indexOf(h);if(g===-1||f===-1){if(g===f){return[]}return(g===-1)?([h]):([i])}return(g<f)?this.views.slice(g,f+1):this.views.slice(f,g+1)},_renderSearch:function(f){f.find(".controls .search-input").searchInput({placeholder:this.searchPlaceholder,initialVal:this.searchFor,onfirstsearch:_.bind(this._firstSearch,this),onsearch:_.bind(this.searchItems,this),onclear:_.bind(this.clearSearch,this)});return f},_firstSearch:function(f){this.log("onFirstSearch",f);return this.searchItems(f)},searchItems:function(f){this.searchFor=f;this.trigger("search:searching",f,this);this.renderItems();return this},clearSearch:function(f){this.searchFor="";this.trigger("search:clear",this);this.renderItems();return this},showSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=true;this.$(".list-actions").slideDown(f);_.each(this.views,function(g){g.showSelector(f)})},hideSelectors:function(f){f=(f!==undefined)?(f):(this.fxSpeed);this.selecting=false;this.$(".list-actions").slideUp(f);_.each(this.views,function(g){g.hideSelector(f)});this.selected=[];this.lastSelected=null},toggleSelectors:function(){if(!this.selecting){this.showSelectors()}else{this.hideSelectors()}},selectAll:function(f){_.each(this.views,function(g){g.select(f)})},deselectAll:function(f){this.lastSelected=null;_.each(this.views,function(g){g.deselect(f)})},selectRange:function(h,g){var f=this.viewRange(h,g);_.each(f,function(i){i.select()});return f},getSelectedViews:function(){return _.filter(this.views,function(f){return f.selected})},getSelectedModels:function(){return new this.collection.constructor(_.map(this.getSelectedViews(),function(f){return f.model}))},_showLoadingIndicator:function(g,f,h){this.debug("_showLoadingIndicator",this.indicator,g,f,h);f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent());this.debug("\t created",this.indicator)}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},_hideLoadingIndicator:function(f,g){this.debug("_hideLoadingIndicator",this.indicator,f,g);f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},scrollPosition:function(){return this.$scrollContainer().scrollTop()},scrollTo:function(g,f){f=f||0;this.$scrollContainer().animate({scrollTop:g},f);return this},scrollToTop:function(f){return this.scrollTo(0,f)},scrollToItem:function(f,h){if(!f){return this}var g=f.$el.position().top;return this.scrollTo(g,h)},scrollToId:function(g,f){return this.scrollToItem(this.viewFromModelId(g),f)},events:{"click .select-all":"selectAll","click .deselect-all":"deselectAll"},toString:function(){return"ListPanel("+this.collection+")"}});e.prototype.templates=(function(){var g=b.wrapTemplate(["<div>",'<div class="controls"></div>','<div class="list-items"></div>','<div class="empty-message infomessagesmall"></div>',"</div>"]);var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= view.title %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return{el:g,controls:f}}());var a=e.extend({modelCollectionKey:"contents",initialize:function(f){e.prototype.initialize.call(this,f);this.selecting=(f.selecting!==undefined)?f.selecting:false;this.setModel(this.model,f)},setModel:function(g,f){f=f||{};this.debug(this+".setModel:",g,f);this.freeModel();this.freeViews();if(g){var h=this.model?this.model.get("id"):null;this.model=g;if(this.logger){this.model.logger=this.logger}this._setUpModelListeners();this.collection.off();this.collection=(this.model[this.modelCollectionKey])?this.model[this.modelCollectionKey]:(f.collection||(new this.collectionClass([])));this._setUpCollectionListeners();if(h&&g.get("id")!==h){this.trigger("new-model",this)}}return this},freeModel:function(){if(this.model){this.stopListening(this.model)}return this},_setUpModelListeners:function(){this.log(this+"._setUpModelListeners",this.model);this.model.on("error",function(){this.trigger.apply(panel,arguments)},this);return this},_renderControls:function(g){this.debug(this+"(ListPanel)._renderControls");var h=this.model?this.model.toJSON():{},f=$(this.templates.controls(h,this));g.find(".controls").replaceWith(f);return f},toString:function(){return"ModelListPanel("+this.model+")"}});a.prototype.templates=(function(){var f=b.wrapTemplate(['<div class="controls">','<div class="title">','<div class="name"><%= model.name %></div>',"</div>",'<div class="subtitle"><%= view.subtitle %></div>','<div class="actions"></div>','<div class="messages"></div>','<div class="search">','<div class="search-input"></div>',"</div>",'<div class="list-actions">','<div class="btn-group">','<button class="select-all btn btn-default"','data-mode="select">',c("All"),"</button>",'<button class="deselect-all btn btn-default"','data-mode="select">',c("None"),"</button>","</div>","</div>","</div>"]);return _.extend(_.clone(e.prototype.templates),{controls:f})}());return{ListPanel:e,ModelListPanel:a}}); \ No newline at end of file diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1834,8 +1834,7 @@ .icon-button.link{background:url(../images/silk/link.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px} .icon-button.link-broken{background:url(../images/silk/link_break.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px} .workflow-invocation-complete{border:solid 1px #6A6;border-left-width:5px;margin:10px 0;padding-left:5px} -.icon-btn,.ui-button-icon,.ui-button-icon-plain{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;border-radius:3px;border:1px solid #bfbfbf;background-color:#f2f2f2;color:#333;cursor:pointer} -.icon-btn:hover{background-color:white;color:maroon} +.icon-btn,.ui-button-icon,.ui-button-icon-plain{display:inline-block;height:22px;width:22px;text-align:center;line-height:19px;font-size:1.2em;border-radius:3px;border:1px solid #bfbfbf;background-color:#f2f2f2;color:#333;cursor:pointer}.icon-btn:focus,.icon-btn:hover{outline:0;background-color:white;color:maroon} .icon-btn.disabled{background-color:transparent;color:#BBB;border-color:#BBB} .icon-btn-group{display:inline-block}.icon-btn-group .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} .icon-btn-group .icon-btn:first-child{margin-right:0px;border-top-left-radius:3px;border-bottom-left-radius:3px} @@ -1969,7 +1968,8 @@ .annotated-history-panel table.list-items>tbody>tr>td:nth-child(2){padding:8px 16px 8px 16px;white-space:pre-wrap} .annotated-history-panel table.list-items>tbody>tr>td>.list-item{border:0px} .annotated-history-panel .empty-message{margin-top:8px} -.current-history-panel .list-item.history-content.current-content{border:2px solid black;border-bottom-width:2px}.current-history-panel .list-item.history-content.current-content .title-bar{padding:5px 8px 6px 6px} +.current-history-panel .list-item.history-content.current-content{border:2px solid #333;border-bottom-width:2px}.current-history-panel .list-item.history-content.current-content .primary-actions{margin:5px 8px 0px 0px} +.current-history-panel .list-item.history-content.current-content .title-bar{padding:5px 8px 5px 6px} .current-history-panel .list-item.history-content.current-content .details{padding:0px 8px 5px 6px} body.historyPage{background:#dfe5f9;color:#000;margin:5px;border:0;padding:0} div.historyLinks{margin:5px 5px} diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -455,16 +455,14 @@ -.quota-meter-container -{ +.quota-meter-container { position: absolute; top: 0; right: 0; height: 32px; } -.quota-meter -{ +.quota-meter { position: absolute; top: 8px; right: 8px; @@ -473,8 +471,7 @@ background-color: @progress-bg; } -.quota-meter-bar -{ +.quota-meter-bar { position: absolute; top: 0; left: 0; @@ -482,18 +479,15 @@ background-color: @brand-primary; } -.quota-meter-bar-warn -{ +.quota-meter-bar-warn { background-color: @brand-warning; } -.quota-meter-bar-error -{ +.quota-meter-bar-error { background-color: @brand-danger; } -.quota-meter-text -{ +.quota-meter-text { position: absolute; top: 50%; left: 0; diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -590,25 +590,14 @@ // ---------------------------------------------------------------------------- current-history-panel .current-history-panel { .list-item.history-content.current-content { - //border-top: 2px solid black; - //border-right: 1px solid black; - //border-bottom: 2px solid black; - //border-left: 1px solid black; - //.title-bar { - // border-color: black; - // background: black; - // color: white; - //} - - //position: relative; - //margin-left: -24px; - //z-index: 1000; - - border: 2px solid black; + border: 2px solid #333; border-bottom-width: 2px; + .primary-actions { + margin: 5px 8px 0px 0px; + } .title-bar { - padding: 5px 8px 6px 6px; + padding: 5px 8px 5px 6px; } .details { padding: 0px 8px 5px 6px; diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/style/src/less/list-item.less --- a/static/style/src/less/list-item.less +++ b/static/style/src/less/list-item.less @@ -73,6 +73,10 @@ word-break: break-all; line-height: 16px; } +//TODO: show keyboard/tab focus for keyboard users + //&:focus { + // color: maroon; + //} } .primary-actions { diff -r 14e656b67cedb9456c37eef5b228962496b4e0b3 -r 6b5dcb4c191805e96d62bddfd5f7fd7ecc61f792 static/style/src/less/ui/icon-btn.less --- a/static/style/src/less/ui/icon-btn.less +++ b/static/style/src/less/ui/icon-btn.less @@ -44,16 +44,13 @@ cursor: pointer; - // tweaks - //TODO: not working - span - //.fa-comment { - // display: inline-block; - // margin-bottom: 4px; - //} -} -.icon-btn:hover { - background-color: white; - color: maroon; + &:focus, + &:hover { + outline: 0; + background-color: white; + color: maroon; + } + } .icon-btn.disabled { background-color: transparent; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Update tag latest_2014.08.11 for changeset 548ab24667d6
by commits-noreply＠bitbucket.org 23 Sep '14

23 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/007f6a80629a/ Changeset: 007f6a80629a Branch: stable User: natefoo Date: 2014-09-23 19:00:18+00:00 Summary: Update tag latest_2014.08.11 for changeset 548ab24667d6 Affected #: 1 file diff -r 548ab24667d6206780237bd807f7d857a484c461 -r 007f6a80629a74650b72d67821a9505932d284f3 .hgtags --- a/.hgtags +++ b/.hgtags @@ -18,4 +18,4 @@ 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 -9f15bf53a11b8a91301381d836271a0ac3b23e71 latest_2014.08.11 +548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

[galaxyproject/usegalaxy-playbook] 234d5c: Updated slides.
by GitHub 23 Sep '14

23 Sep '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 234d5ca4b6dba9d928ff4d56fc648d62c92ff052 https://github.com/galaxyproject/usegalaxy-playbook/commit/234d5ca4b6dba9d9… Author: Dave Clements <clements(a)d92-226.uoregon.edu> Date: 2014-09-23 (Tue, 23 Sep 2014) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slides.

1 0

commit/galaxy-central: guerler: ToolForm: Scrolling to error, basic validation, success message, style fixes
by commits-noreply＠bitbucket.org 23 Sep '14

23 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/14e656b67ced/ Changeset: 14e656b67ced User: guerler Date: 2014-09-23 18:18:45+00:00 Summary: ToolForm: Scrolling to error, basic validation, success message, style fixes Affected #: 15 files diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -17,7 +17,7 @@ // create form view var View = Backbone.View.extend({ // base element - main_el: 'body', + container: 'body', // initialize initialize: function(options) { @@ -27,6 +27,12 @@ // link options this.options = options; + // set element + this.setElement('<div/>'); + + // add to main element + $(this.container).append(this.$el); + // load tool model this.model = new Model({ id : options.id @@ -57,9 +63,9 @@ }, // message - message: function(options) { - $(this.main_el).empty(); - $(this.main_el).append(ToolTemplate.message(options)); + message: function($el) { + $(this.container).empty(); + $(this.container).append($el); }, // reset form @@ -156,17 +162,17 @@ } // append form - $(self.main_el).append(self.portlet.$el); + self.$el.append(self.portlet.$el); // append help if (self.options.help != '') { - $(self.main_el).append(ToolTemplate.help(self.options.help)); + self.$el.append(ToolTemplate.help(self.options.help)); } // append citations if (self.options.citations) { // append html - $(self.main_el).append(ToolTemplate.citations()); + self.$el.append(ToolTemplate.citations()); // fetch citations var citations = new CitationModel.ToolCitationCollection(); diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -1,7 +1,7 @@ /** This class handles job submissions and the error handling. */ -define(['utils/utils'], function(Utils) { +define(['utils/utils', 'mvc/tools/tools-template'], function(Utils, ToolTemplate) { return Backbone.Model.extend({ // initialize initialize: function(app, options) { @@ -37,12 +37,7 @@ Utils.request('POST', galaxy_config.root + 'api/tools', job_def, // success handler function(response) { - if (!response.outputs || response.outputs.length == 0) { - console.debug(response); - } - self.app.message({ - text : 'A job has been successfully added to the queue. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.' - }); + self.app.message(ToolTemplate.success(response)); self._refreshHdas(); }, // error handler @@ -77,16 +72,25 @@ var input = job_inputs[job_input_id]; var input_id = this.app.tree.match(job_input_id); var input_field = this.app.field_list[input_id]; + var input_element = this.app.element_list[input_id]; // check field validation - //if (input_field && input_field.validate && !input_field.validate()) { + if (input && !input.optional && input_field && input_field.validate && !input_field.validate()) { this.app.element_list[input_id].error('Please verify this parameter.'); - valid = false; - //} + if (valid) { + // scroll to first input element + $(this.app.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + + // validation failed + valid = false; + } + } } // return result - return false; + return valid; }, /** Refreshes the history panel diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -15,10 +15,29 @@ return '<div id="citations"></div>'; }, - message: function(options) { - return '<div class="donemessagelarge">' + - '<p>' + options.text + '</p>' + - '</div>'; + success: function(response) { + // number of jobs + var njobs = response.jobs.length; + + // job count info text + var njobs_text = ''; + if (njobs == 1) { + njobs_text = '1 job has'; + } else { + njobs_text = njobs + ' jobs have been'; + } + + // create template string + var tmpl = '<div class="donemessagelarge">' + + '<p>' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:</p>'; + for (var i in response.outputs) { + tmpl += '<p style="padding: 10px 20px;"><b>' + (parseInt(i)+1) + ': ' + response.outputs[i].name + '</b></p>'; + } + tmpl += '<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.</p>' + + '</div>'; + + // return success message element + return tmpl; } }; diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 client/galaxy/scripts/mvc/ui/ui-portlet.js --- a/client/galaxy/scripts/mvc/ui/ui-portlet.js +++ b/client/galaxy/scripts/mvc/ui/ui-portlet.js @@ -158,13 +158,13 @@ if (options.title) { tmpl += '<div id="portlet-header" class="portlet-header">' + '<div id="operations" style="float: right;"></div>' + - '<h3 class="portlet-title">'; + '<div class="portlet-title">'; if (options.icon) tmpl += '<i class="icon fa ' + options.icon + '"> </i>'; tmpl += '<span id="portlet-title-text" class="portlet-title-text">' + options.title + '</span>' + - '</h3>' + + '</div>' + '</div>'; } tmpl += '<div id="portlet-content" class="portlet-content">'; diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).hide()},getButton:function(e){var t=this.buttonList[e];return this.$buttons.find("#"+t)},scrollTop:function(){return this.$body.scrollTop()},_create:function(e){var t=this;this.options=_.defaults(e,this.optionsDefault),this.options.body=="progress"&&(this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')),this.$el&&(this.$el.remove(),$(document).off("keyup.ui-modal")),this.setElement(this._template(this.options.title)),this.$dialog=this.$el.find(".modal-dialog"),this.$body=this.$el.find(".modal-body"),this.$footer=this.$el.find(".modal-footer"),this.$buttons=this.$el.find(".buttons"),this.$backdrop=this.$el.find(".modal-backdrop"),this.$body.html(this.options.body),this.options.backdrop||this.$backdrop.removeClass("in");if(this.options.buttons){this.buttonList={};var n=0;$.each(this.options.buttons,function(e,r){var i="button-"+n++;t.$buttons.append($('<button id="'+i+'"></button>').text(e).click(r)).append(" "),t.buttonList[e]=i})}else this.$footer.hide();$(this.elMain).append($(this.el)),this.options.closing_events&&($(document).on("keyup.ui-modal",function(e){e.keyCode==27&&t.hide()}),this.$el.find(".modal-backdrop").on("click",function(){t.hide()}))},_template:function(e){return'<div class="ui-modal modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+e+"</h4>"+"</div>"+'<div class="modal-body" style="position: static;"></div>'+'<div class="modal-footer">'+'<div class="buttons" style="float: right;"></div>'+"</div>"+"</div"+"</div>"+"</div>"}});return{View:e}}),function(){var 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e!==undefined&&this.$select.val(e),this.$select.val()},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){var t=this.$select.val();this.$select.find("option").remove();for(var n in e)this.$select.append(this._templateOption(e[n]));this._refresh(),this.$select.val(t),this.$select.val()||this.$select.val(this.first())},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find('option[value="'+e+'"]').length>0},_change:function(){this.options.onchange&&this.options.onchange(this.$select.val())},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable()},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){return'<div id="'+e.id+'">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'"></select>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-slider",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{value:"",min:1,max:100,step:1},initialize:function(t){var n=this;this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$slider=this.$el.find("#slider"),this.$text=this.$el.find("#text"),this.$slider.slider(this.options),this.$text.on("change",function(){n.value($(this).val())}),this.$text.on("keydown",function(e){var t=e.which;t==13||t==8||t==37||t==39||t==189||t>=48&&t<=57||n.options.step!=1&&$(this).val().indexOf(".")==-1&&t==190||e.preventDefault()}),this.$slider.on("slide",function(e,t){n.value(t.value)})},value:function(e){return e!==undefined&&(e=Math.max(Math.min(e,this.options.max),this.options.min),this.options.onchange&&this.options.onchange(e),this.$slider.slider("value",e),this.$text.val(e)),this.$text.val()},_template:function(e){return'<div id="'+e.id+'" class="ui-form-slider">'+'<input id="text" type="text" class="ui-form-slider-text"/>'+'<div id="slider" class="ui-form-slider-element"/>'+"</div>"}});return{View:t}}),define("mvc/ui/ui-options",["utils/utils"],function(e){var t=Backbone.View.extend({initialize:function(t){this.optionsDefault={value:[],visible:!0,data:[],id:e.uuid(),empty:"No data available"},this.options=e.merge(t,this.optionsDefault),this.setElement("<div/>"),this.$error=$(this._templateError(t)),this.$options=$(this._template(t)),this.$el.append(this.$error),this.$el.append(this.$options),this.options.visible||this.$el.hide(),this.update(this.options.data),this.options.value&&this.value(this.options.value);var n=this;this.on("change",function(){n._change()})},update:function(e){var t=this._getValue();this.$el.find(".ui-option").remove();for(var n in e){var r=$(this._templateOption(e[n]));r.addClass("ui-option"),this.$options.append(r)}var i=this;this.$el.find("input").on("change",function(){i.value(i._getValue()),i._change()}),this._refresh(),this.value(t)},exists:function(e){typeof e=="string"&&(e=[e]);for(var t in e)if(this.$el.find('input[value="'+e[t]+'"]').length>0)return!0;return!1},first:function(){var e=this.$el.find("input");return e.length>0?e.val():undefined},_change:function(){this.options.onchange&&this.options.onchange(this._getValue())},_refresh:function(){var e=this.$el.find(".ui-option").length;e==0?(this.$error.show(),this.$options.hide()):(this.$error.hide(),this.$options.css("display","inline-block"))},_getValue:function(){var e=this.$el.find(":checked");if(e.length==0)return null;if(this.options.multiple){var t=[];return e.each(function(){t.push($(this).val())}),t}return e.val()},_templateError:function(e){return'<div class="ui-error" style="display: none;">'+e.empty+"</div>"}}),n={};n.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){typeof e=="string"&&(e=[e]);if(e!==undefined){this.$el.find("input").prop("checked",!1);for(var t in e)this.$el.find("input[value="+e[t]+"]").prop("checked",!0)}return this._getValue()},_templateOption:function(e){return'<div><input type="radio" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"},_template:function(){return'<div class="ui-options"/>'}});var r={};r.View=n.View.extend({initialize:function(e){e.multiple=!0,n.View.prototype.initialize.call(this,e)},_templateOption:function(e){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+e.value+'"/>'+e.label+"<br>"+"</div>"}});var i={};return i.View=t.extend({initialize:function(e){t.prototype.initialize.call(this,e)},value:function(e){return e!==undefined&&(this.$el.find("input").prop("checked",!1),this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').prop("checked",!0).closest("label").addClass("active")),this._getValue()},_templateOption:function(e){var t='<label class="btn btn-default">';return e.icon&&(t+='<i class="fa '+e.icon+'"/>'),t+='<input type="radio" name="'+this.options.id+'" value="'+e.value+'">'+e.label+"</label>",t},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}}),{Radio:n,RadioButton:i,Checkbox:r}}),define("mvc/ui/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"",floating:"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("mvc/ui/ui-misc",["utils/utils","mvc/ui/ui-select-default","mvc/ui/ui-slider","mvc/ui/ui-options","mvc/ui/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r,i,s){var o=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),u=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),a=Backbone.View.extend({optionsDefault:{floating:"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),f=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.floating+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),l=Backbone.View.extend({optionsDefault:{id:null,title:"",floating:"right",cls:"ui-button-icon",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.$button=this.$el.find(".button");var n=this;$(this.el).on("click",function(){$(".tooltip").hide(),t.onclick&&!n.disabled&&t.onclick()}),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},disable:function(){this.$button.addClass("disabled"),this.disabled=!0},enable:function(){this.$button.removeClass("disabled"),this.disabled=!1},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.floating+"; "+t+'" class="'+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),c=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),h=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new 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title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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alert-'+e.status+'"/>'}}),p=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),d=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:"",area:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return e.area?'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'"></textarea>':'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),v=Backbone.View.extend({optionsDefault:{value:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<hidden id="'+e.id+'" value="'+e.value+'"/>'}});return{Anchor:c,Button:f,ButtonIcon:l,ButtonMenu:i,Icon:a,Image:o,Input:d,Label:u,Message:h,Modal:s,RadioButton:r.RadioButton,Checkbox:r.Checkbox,Radio:r.Radio,Searchbox:p,Select:t,Hidden:v,Slider:n}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null,max:null,onchange:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.current_id=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},size:function(){return _.size(this.list)},current:function(){return this.$el.find(".tab-pane.active").attr("id")},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),this.size()==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n),this.options.max&&this.size()>=this.options.max&&this.$el.find("#new-tab").hide();if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)}),this.current_id||(this.current_id=n)},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab),this.list[e]&&delete this.list[e],this.size()<this.options.max&&this.$el.find("#new-tab").show()},delRemovable:function(){for(var e in this.list)this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find("#tab-"+this.current_id).removeClass("active"),this.$el.find("#"+this.current_id).removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#"+e).addClass("active"),this.current_id=e),this.options.onchange&&this.options.onchange(e)},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},retitle:function(e){var t=0;for(var n in this.list)this.title(n,++t+": "+e)},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'" class="tab-title-text">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("mvc/ui/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:"ui-table",cls_tr:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=this._row()},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e,t){this._commit(e,t,!1)},prepend:function(e,t){this._commit(e,t,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t,n){this.del(e),this.row.attr("id",e),n?this.$tbody.prepend(this.row):this.$tbody.append(this.row),t&&(this.row.hide(),this.row.fadeIn()),this.row=this._row(),this.row_count++,this._refresh()},_row:function(){return $('<tr class="'+this.options.cls_tr+'"></tr>')},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="'+e.cls+'">'+"<thead></thead>"+"<tbody></tbody>"+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["mvc/ui/ui-table","mvc/ui/ui-misc","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["mvc/ui/ui-misc","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","mvc/ui/ui-misc"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton.View({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small"),this.library.trigger("change")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var e=0,t=this.app.types.attributes;for(var n in t){var r=t[n],i=r.category;this.categories[i]||(this.categories[i]={},this.categories_index[i]=e++),this.categories[i][n]=r}for(var i in this.categories){var s=$('<div style="clear: both;"/>');s.append(this._template_header({id:"types-header-"+this.categories_index[i],title:i}));for(var n in this.categories[i]){var r=this.categories[i][n],o=r.title+" ("+r.library+")";r.zoomable&&(o='<span class="fa fa-search-plus"/>'+o),s.append(this._template_item({id:n,title:o,url:config.app_root+"charts/"+this.app.chartPath(n)+"/logo.png"}))}this.$el.append(s)}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","mvc/ui/ui-misc","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+o.left,e.pos[1]+o.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){v&&e.tooltip.cleanup()}),N.dispatch=S,N.lines=t,N.legend=i,N.xAxis=n,N.yAxis=r,N.interactiveLayer=s,d3.rebind(N,t,"defined","isArea","x","y","size","xScale","yScale","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","useVoronoi","id","interpolate"),N.options=e.utils.optionsFunc.bind(N),N.margin=function(e){return arguments.length?(o.top=typeof e.top!="undefined"?e.top:o.top,o.right=typeof e.right!="undefined"?e.right:o.right,o.bottom=typeof e.bottom!="undefined"?e.bottom:o.bottom,o.left=typeof e.left!="undefined"?e.left:o.left,N):o},N.width=function(e){return arguments.length?(a=e,N):a},N.height=function(e){return arguments.length?(f=e,N):f},N.color=function(t){return 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l=d3.select(this),c=this,v=(a||parseInt(l.style("width"))||960)-u.left-u.right,N=(f||parseInt(l.style("height"))||400)-u.top-u.bottom;T.update=function(){l.call(T)},b.disabled=e.map(function(e){return!!e.disabled});if(!w){var C;w={};for(C in b)b[C]instanceof Array?w[C]=b[C].slice(0):w[C]=b[C]}if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var k=l.selectAll(".nv-noData").data([E]);return k.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),k.attr("x",u.left+v/2).attr("y",u.top+N/2).text(function(e){return e}),T}l.selectAll(".nv-noData").remove();var L=e.filter(function(e){return!e.disabled&&e.bar}),A=e.filter(function(e){return!e.bar});m=A.filter(function(e){return!e.disabled}).length&&A.filter(function(e){return!e.disabled})[0].values.length?t.xScale():n.xScale(),g=n.yScale(),y=t.yScale();var O=d3.select(this).selectAll("g.nv-wrap.nv-linePlusBar").data([e]),M=O.enter().append("g").attr("class","nvd3 nv-wrap 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D=_.select(".nv-barsWrap").datum(L.length?L:[{values:[]}]),P=_.select(".nv-linesWrap").datum(A[0]&&!A[0].disabled?A:[{values:[]}]);d3.transition(D).call(n),d3.transition(P).call(t),r.scale(m).ticks(v/100).tickSize(-N,0),_.select(".nv-x.nv-axis").attr("transform","translate(0,"+g.range()[0]+")"),d3.transition(_.select(".nv-x.nv-axis")).call(r),i.scale(g).ticks(N/36).tickSize(-v,0),d3.transition(_.select(".nv-y1.nv-axis")).style("opacity",L.length?1:0).call(i),s.scale(y).ticks(N/36).tickSize(L.length?0:-v,0),_.select(".nv-y2.nv-axis").style("opacity",A.length?1:0).attr("transform","translate("+v+",0)"),d3.transition(_.select(".nv-y2.nv-axis")).call(s),o.dispatch.on("stateChange",function(e){b=e,S.stateChange(b),T.update()}),S.on("tooltipShow",function(e){d&&x(e,c.parentNode)}),S.on("changeState",function(t){typeof t.disabled!="undefined"&&(e.forEach(function(e,n){e.disabled=t.disabled[n]}),b.disabled=t.disabled),T.update()})}),T}var t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var n=g(e[0])-v.range()[0],r=v.range()[1]-g(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",g(e[1])).attr("width",r<0?0:r)})}function z(){w=a.empty()?null:a.extent();var n=a.empty()?g.domain():a.extent();if(Math.abs(n[0]-n[1])<=1)return;T.brush({extent:n,brush:a}),U();var s=P.select(".nv-focus .nv-linesWrap").datum(e.filter(function(e){return!e.disabled}).map(function(e,r){return{key:e.key,values:e.values.filter(function(e,r){return t.x()(e,r)>=n[0]&&t.x()(e,r)<=n[1]})}}));s.call(t),P.select(".nv-focus .nv-x.nv-axis").call(r),P.select(".nv-focus .nv-y.nv-axis").call(i)}var S=d3.select(this),N=this,L=(h||parseInt(S.style("width"))||960)-f.left-f.right,A=(p||parseInt(S.style("height"))||400)-f.top-f.bottom-d,O=d-l.top-l.bottom;k.update=function(){S.call(k)},k.container=this;if(!e||!e.length||!e.filter(function(e){return e.values.length}).length){var M=S.selectAll(".nv-noData").data([x]);return M.enter().append("text").attr("class","nvd3 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var 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s,a,f,c=[];y.filter(function(e,t){return e.seriesIndex=t,!e.disabled}).forEach(function(n,r){a=e.interactiveBisect(n.values,i.pointXValue,M.x()),t.highlightPoint(r,a,!0);var o=n.values[a];if(typeof o=="undefined")return;typeof s=="undefined"&&(s=o),typeof f=="undefined"&&(f=M.xScale()(M.x()(o,a)));var u=t.style()=="expand"?o.display.y:M.y()(o,a);c.push({key:n.key,value:u,color:l(n,n.seriesIndex),stackedValue:o.display})}),c.reverse();if(c.length>2){var h=M.yScale().invert(i.mouseY),p=Infinity,d=null;c.forEach(function(e,t){h=Math.abs(h);var n=Math.abs(e.stackedValue.y0),r=Math.abs(e.stackedValue.y);if(h>=n&&h<=r+n){d=t;return}}),d!=null&&(c[d].highlight=!0)}var v=n.tickFormat()(M.x()(s,a)),m=t.style()=="expand"?function(e,t){return d3.format(".1%")(e)}:function(e,t){return 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\ No newline at end of file diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -17,7 +17,7 @@ // create form view var View = Backbone.View.extend({ // base element - main_el: 'body', + container: 'body', // initialize initialize: function(options) { @@ -27,6 +27,12 @@ // link options this.options = options; + // set element + this.setElement('<div/>'); + + // add to main element + $(this.container).append(this.$el); + // load tool model this.model = new Model({ id : options.id @@ -57,9 +63,9 @@ }, // message - message: function(options) { - $(this.main_el).empty(); - $(this.main_el).append(ToolTemplate.message(options)); + message: function($el) { + $(this.container).empty(); + $(this.container).append($el); }, // reset form @@ -156,17 +162,17 @@ } // append form - $(self.main_el).append(self.portlet.$el); + self.$el.append(self.portlet.$el); // append help if (self.options.help != '') { - $(self.main_el).append(ToolTemplate.help(self.options.help)); + self.$el.append(ToolTemplate.help(self.options.help)); } // append citations if (self.options.citations) { // append html - $(self.main_el).append(ToolTemplate.citations()); + self.$el.append(ToolTemplate.citations()); // fetch citations var citations = new CitationModel.ToolCitationCollection(); diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -1,7 +1,7 @@ /** This class handles job submissions and the error handling. */ -define(['utils/utils'], function(Utils) { +define(['utils/utils', 'mvc/tools/tools-template'], function(Utils, ToolTemplate) { return Backbone.Model.extend({ // initialize initialize: function(app, options) { @@ -37,12 +37,7 @@ Utils.request('POST', galaxy_config.root + 'api/tools', job_def, // success handler function(response) { - if (!response.outputs || response.outputs.length == 0) { - console.debug(response); - } - self.app.message({ - text : 'A job has been successfully added to the queue. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.' - }); + self.app.message(ToolTemplate.success(response)); self._refreshHdas(); }, // error handler @@ -77,16 +72,25 @@ var input = job_inputs[job_input_id]; var input_id = this.app.tree.match(job_input_id); var input_field = this.app.field_list[input_id]; + var input_element = this.app.element_list[input_id]; // check field validation - //if (input_field && input_field.validate && !input_field.validate()) { + if (input && !input.optional && input_field && input_field.validate && !input_field.validate()) { this.app.element_list[input_id].error('Please verify this parameter.'); - valid = false; - //} + if (valid) { + // scroll to first input element + $(this.app.container).animate({ + scrollTop: input_element.$el.offset().top - 20 + }, 500); + + // validation failed + valid = false; + } + } } // return result - return false; + return valid; }, /** Refreshes the history panel diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -15,10 +15,29 @@ return '<div id="citations"></div>'; }, - message: function(options) { - return '<div class="donemessagelarge">' + - '<p>' + options.text + '</p>' + - '</div>'; + success: function(response) { + // number of jobs + var njobs = response.jobs.length; + + // job count info text + var njobs_text = ''; + if (njobs == 1) { + njobs_text = '1 job has'; + } else { + njobs_text = njobs + ' jobs have been'; + } + + // create template string + var tmpl = '<div class="donemessagelarge">' + + '<p>' + njobs_text + ' been successfully added to the queue - resulting in the following datasets:</p>'; + for (var i in response.outputs) { + tmpl += '<p style="padding: 10px 20px;"><b>' + (parseInt(i)+1) + ': ' + response.outputs[i].name + '</b></p>'; + } + tmpl += '<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.</p>' + + '</div>'; + + // return success message element + return tmpl; } }; diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/scripts/mvc/ui/ui-portlet.js --- a/static/scripts/mvc/ui/ui-portlet.js +++ b/static/scripts/mvc/ui/ui-portlet.js @@ -158,13 +158,13 @@ if (options.title) { tmpl += '<div id="portlet-header" class="portlet-header">' + '<div id="operations" style="float: right;"></div>' + - '<h3 class="portlet-title">'; + '<div class="portlet-title">'; if (options.icon) tmpl += '<i class="icon fa ' + options.icon + '"> </i>'; tmpl += '<span id="portlet-title-text" class="portlet-title-text">' + options.title + '</span>' + - '</h3>' + + '</div>' + '</div>'; } tmpl += '<div id="portlet-content" class="portlet-content">'; diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(h,l,j,a,f,d,i,k,c,g){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(n){var m=this;this.options=n;this.model=new e({id:n.id});this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.datasets=new i({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.main_el).empty();$(this.main_el).append(d.message(m))},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_initializeToolForm:function(){var n=this;var o=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var p=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});this.model.fetch({error:function(q){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");n.portlet=new h.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})},operations:{button_question:o,button_search:p,button_share:m}});if(!n.options.biostar_url){o.$el.hide();p.$el.hide()}$(n.main_el).append(n.portlet.$el);if(n.options.help!=""){$(n.main_el).append(d.help(n.options.help))}if(n.options.citations){$(n.main_el).append(d.citations());var q=new j.ToolCitationCollection();q.tool_id=n.options.id;var r=new a.CitationListView({collection:q});r.render();q.fetch()}n.setElement(n.portlet.content());n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}}); \ No newline at end of file +define(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(h,l,j,a,f,d,i,k,c,g){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id});this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.datasets=new i({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated tree structure. Refresh.")},_initializeToolForm:function(){var n=this;var o=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var p=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});this.model.fetch({error:function(q){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");n.portlet=new h.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),buttons:{execute:new l.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){n.job_handler.submit()}})},operations:{button_question:o,button_search:p,button_share:m}});if(!n.options.biostar_url){o.$el.hide();p.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var q=new j.ToolCitationCollection();q.tool_id=n.options.id;var r=new a.CitationListView({collection:q});r.render();q.fetch()}n.setElement(n.portlet.content());n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}}); \ No newline at end of file diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(c,b){this.app=c;this.options=a.merge(b,this.optionsDefault)},submit:function(){var b=this;var c={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(c)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}a.request("POST",galaxy_config.root+"api/tools",c,function(d){if(!d.outputs||d.outputs.length==0){console.debug(d)}b.app.message({text:"A job has been successfully added to the queue. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered."});b._refreshHdas()},function(d){console.debug(d);if(d&&d.message&&d.message.data){var g=b.app.tree.matchResponse(d.message.data);for(var f in g){var e=g[f];if(!e){e="Please verify this parameter."}b.app.element_list[f].error(e)}}})},_validation:function(g){var d=g.inputs;var f=true;for(var h in d){var c=d[h];var e=this.app.tree.match(h);var b=this.app.field_list[e];this.app.element_list[e].error("Please verify this parameter.");f=false}return false},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}b.request("POST",galaxy_config.root+"api/tools",d,function(e){c.app.message(a.success(e));c._refreshHdas()},function(e){console.debug(e);if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var g in h){var f=h[g];if(!f){f="Please verify this parameter."}c.app.element_list[g].error(f)}}})},_validation:function(h){var e=h.inputs;var g=true;for(var j in e){var d=e[j];var f=this.app.tree.match(j);var c=this.app.field_list[f];var i=this.app.element_list[f];if(d&&!d.optional&&c&&c.validate&&!c.validate()){this.app.element_list[f].error("Please verify this parameter.");if(g){$(this.app.container).animate({scrollTop:i.$el.offset().top-20},500);g=false}}}return g},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},message:function(a){return'<div class="donemessagelarge"><p>'+a.text+"</p></div>"}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b}}}); \ No newline at end of file diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/scripts/packed/mvc/ui/ui-portlet.js --- a/static/scripts/packed/mvc/ui/ui-portlet.js +++ b/static/scripts/packed/mvc/ui/ui-portlet.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:true,nopadding:false,operations:null,placement:"bottom",cls:"ui-portlet"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(e){this.options=a.merge(e,this.optionsDefault);this.setElement(this._template(this.options));this.$content=this.$el.find("#content");this.$title=this.$el.find("#portlet-title-text");var d=this.$el.find("#portlet-content");if(!this.options.scrollable){if(this.options.title){d.addClass("no-scroll")}else{d.addClass("no-scroll-no-title")}}else{d.addClass("scroll")}if(this.options.nopadding){d.css("padding","0px");this.$content.css("padding","0px")}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(f,g){g.$el.prop("id",f);c.$buttons.append(g.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(f,g){g.$el.prop("id",f);c.$operations.append(g.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},title:function(d){var c=this.$title;if(d){c.html(d)}return c.html()},_template:function(d){var c='<div id="'+d.id+'" class="'+d.cls+'">';if(d.title){c+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3 class="portlet-title">';if(d.icon){c+='<i class="icon fa '+d.icon+'"> </i>'}c+='<span id="portlet-title-text" class="portlet-title-text">'+d.title+"</span></h3></div>"}c+='<div id="portlet-content" class="portlet-content">';if(d.placement=="top"){c+='<div id="buttons" class="buttons"></div>'}c+='<div id="content" class="content"></div>';if(d.placement=="bottom"){c+='<div id="buttons" class="buttons"></div>'}c+="</div></div>";return c}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({visible:false,optionsDefault:{title:"",icon:"",buttons:null,body:null,scrollable:true,nopadding:false,operations:null,placement:"bottom",cls:"ui-portlet"},$title:null,$content:null,$buttons:null,$operations:null,initialize:function(e){this.options=a.merge(e,this.optionsDefault);this.setElement(this._template(this.options));this.$content=this.$el.find("#content");this.$title=this.$el.find("#portlet-title-text");var d=this.$el.find("#portlet-content");if(!this.options.scrollable){if(this.options.title){d.addClass("no-scroll")}else{d.addClass("no-scroll-no-title")}}else{d.addClass("scroll")}if(this.options.nopadding){d.css("padding","0px");this.$content.css("padding","0px")}this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var c=this;$.each(this.options.buttons,function(f,g){g.$el.prop("id",f);c.$buttons.append(g.$el)})}else{this.$buttons.remove()}this.$operations=$(this.el).find("#operations");if(this.options.operations){var c=this;$.each(this.options.operations,function(f,g){g.$el.prop("id",f);c.$operations.append(g.$el)})}if(this.options.body){this.append(this.options.body)}},append:function(c){this.$content.append(a.wrap(c))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast");this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},enableButton:function(c){this.$buttons.find("#"+c).prop("disabled",false)},disableButton:function(c){this.$buttons.find("#"+c).prop("disabled",true)},hideOperation:function(c){this.$operations.find("#"+c).hide()},showOperation:function(c){this.$operations.find("#"+c).show()},setOperation:function(e,d){var c=this.$operations.find("#"+e);c.off("click");c.on("click",d)},title:function(d){var c=this.$title;if(d){c.html(d)}return c.html()},_template:function(d){var c='<div id="'+d.id+'" class="'+d.cls+'">';if(d.title){c+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><div class="portlet-title">';if(d.icon){c+='<i class="icon fa '+d.icon+'"> </i>'}c+='<span id="portlet-title-text" class="portlet-title-text">'+d.title+"</span></div></div>"}c+='<div id="portlet-content" class="portlet-content">';if(d.placement=="top"){c+='<div id="buttons" class="buttons"></div>'}c+='<div id="content" class="content"></div>';if(d.placement=="bottom"){c+='<div id="buttons" class="buttons"></div>'}c+="</div></div>";return c}});return{View:b}}); \ No newline at end of file diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1296,12 +1296,12 @@ .ui-button-icon-plain{border:none !important;background:none !important} .ui-tabs .ui-tabs-add{font-size:0.8em;margin-right:5px} .ui-tabs .ui-tabs-delete{font-size:0.8em;margin-left:5px;cursor:pointer} -.ui-portlet,.ui-portlet-repeat,.ui-portlet-repeat{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header h1,.ui-portlet .portlet-header h2,.ui-portlet .portlet-header h3,.ui-portlet .portlet-header h4,.ui-portlet .portlet-header h5,.ui-portlet .portlet-header h6{float:left;font-weight:normal;display:inline-block;vertical-align:middle;font-size:1em;margin:3px}.ui-portlet .portlet-header h1 .icon,.ui-portlet .portlet-header h2 .icon,.ui-portlet .portlet-header h3 .icon,.ui-portlet .portlet-header h4 .icon,.ui-portlet .portlet-header h5 .icon,.ui-portlet .portlet-header h6 .icon{font-size:1.2em} +.ui-portlet,.ui-portlet-repeat,.ui-portlet-repeat{border:solid #d6b161 1px;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;position:relative;clear:both;width:auto;height:100%}.ui-portlet .portlet-header{background:#ebd9b2;border-bottom:solid #d6b161 1px;padding:2px 8px;overflow:visible;float:right;width:100%}.ui-portlet .portlet-header .portlet-title .portlet-title-text{vertical-align:middle} +.ui-portlet .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} .ui-portlet .portlet-buttons{height:50px;padding:10px} .ui-portlet .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons{height:50px;padding:10px} .ui-portlet .no-scroll{height:calc(100% - 80px)} -.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:1px 0px 0px 2px} -.ui-portlet-repeat .portlet-title{padding-top:1px} +.ui-portlet-repeat{border:none;border-left:solid 3px #ebd9b2;border-radius:5px}.ui-portlet-repeat .portlet-header{background:#ebd9b2;border-radius:3px;border-bottom-left-radius:0px;padding:0px 2px} .ui-portlet-repeat .portlet-content{padding:0px}.ui-portlet-repeat .portlet-content .content{padding:0px;padding-left:10px} .ui-popover{max-width:700px;display:none}.ui-popover .popover-close{position:absolute;right:10px;top:7px;font-size:1.2em;cursor:pointer} .ui-popover .popover-title{padding:4px 10px} diff -r f69e8502c76500d615d8d98a64ae904b1d328284 -r 14e656b67cedb9456c37eef5b228962496b4e0b3 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -142,16 +142,13 @@ float: right; width:100%; - h1, h2, h3, h4, h5, h6 { - float: left; - font-weight: normal; - display: inline-block; - vertical-align: middle; - font-size: 1em; - margin: 3px; - + .portlet-title { + .portlet-title-text { + vertical-align: middle; + } .icon { font-size: 1.2em; + vertical-align: middle; } } } @@ -192,11 +189,7 @@ background: @form-heading-bg; border-radius: 3px; border-bottom-left-radius: 0px; - padding: 1px 0px 0px 2px; - } - - .portlet-title { - padding-top: 1px; + padding: 0px 2px; } .portlet-content { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 23 Sep '14

23 Sep '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c18dc778dabe/ Changeset: c18dc778dabe Branch: next-stable User: jmchilton Date: 2014-09-23 17:38:25+00:00 Summary: Fix run_tests.sh --with_framework_test_tools for 9a05d1e. Now appends test tools to sample tools instead of to default tools Galaxy would other wise load (config/tool_conf.xml or tool_conf.xml if these exist instead of sample) - so this is different behavior but I am unsure if it is worse. --with_framework_test_tools was added for API tests and these should probably target the distribution and not random tools someone might have configured so perhaps this new behavior is superior. Affected #: 1 file diff -r 6e02e4f954d254787ce9caaf961b0a271bc7bcb6 -r c18dc778dabe708961554170f1af7dd50bd81be0 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -226,9 +226,7 @@ # Use tool_conf.xml toolbox. tool_conf = None if __check_arg( '-with_framework_test_tools' ): - # Some of these tools will not work without swapping - # default interactor to point to test. - tool_conf = "%s,%s" % ( tool_conf, os.path.join( framework_tool_dir, 'samples_tool_conf.xml' ) ) + tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', os.path.join( framework_tool_dir, 'samples_tool_conf.xml' ) ) test_dir = default_galaxy_test_file_dir tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', tool_conf ) galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', test_dir ) https://bitbucket.org/galaxy/galaxy-central/commits/803755d0cd20/ Changeset: 803755d0cd20 Branch: next-stable User: jmchilton Date: 2014-09-23 17:38:25+00:00 Summary: Improved configuration error messages. Affected #: 1 file diff -r c18dc778dabe708961554170f1af7dd50bd81be0 -r 803755d0cd2098165c819c44b81f7f2591f9c69e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -518,9 +518,9 @@ tool_configs.append( self.migrated_tools_config ) for path in tool_configs: if not os.path.exists( path ): - raise ConfigurationError("File not found: %s" % path ) + raise ConfigurationError("Tool config file not found: %s" % path ) if not os.path.isfile( self.datatypes_config ): - raise ConfigurationError("File not found: %s" % self.datatypes_config ) + raise ConfigurationError("Datatypes config file not found: %s" % self.datatypes_config ) # Check for deprecated options. for key in self.config_dict.keys(): if key in self.deprecated_options: https://bitbucket.org/galaxy/galaxy-central/commits/f69e8502c765/ Changeset: f69e8502c765 User: jmchilton Date: 2014-09-23 17:39:09+00:00 Summary: Merge latest next-stable. Affected #: 2 files diff -r 05abe03187a13527b8da8d0421822090a96969a7 -r f69e8502c76500d615d8d98a64ae904b1d328284 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -518,9 +518,9 @@ tool_configs.append( self.migrated_tools_config ) for path in tool_configs: if not os.path.exists( path ): - raise ConfigurationError("File not found: %s" % path ) + raise ConfigurationError("Tool config file not found: %s" % path ) if not os.path.isfile( self.datatypes_config ): - raise ConfigurationError("File not found: %s" % self.datatypes_config ) + raise ConfigurationError("Datatypes config file not found: %s" % self.datatypes_config ) # Check for deprecated options. for key in self.config_dict.keys(): if key in self.deprecated_options: diff -r 05abe03187a13527b8da8d0421822090a96969a7 -r f69e8502c76500d615d8d98a64ae904b1d328284 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -226,9 +226,7 @@ # Use tool_conf.xml toolbox. tool_conf = None if __check_arg( '-with_framework_test_tools' ): - # Some of these tools will not work without swapping - # default interactor to point to test. - tool_conf = "%s,%s" % ( tool_conf, os.path.join( framework_tool_dir, 'samples_tool_conf.xml' ) ) + tool_conf = "%s,%s" % ( 'config/tool_conf.xml.sample', os.path.join( framework_tool_dir, 'samples_tool_conf.xml' ) ) test_dir = default_galaxy_test_file_dir tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', tool_conf ) galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', test_dir ) 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 commits-noreply＠bitbucket.org 23 Sep '14

23 Sep '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6e02e4f954d2/ Changeset: 6e02e4f954d2 Branch: next-stable User: natefoo Date: 2014-09-23 14:40:39+00:00 Summary: Use common_startup.sh for buildbot instead of maintaining a duplicate copy of the samples list. Affected #: 1 file diff -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e -r 6e02e4f954d254787ce9caaf961b0a271bc7bcb6 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -42,17 +42,6 @@ /galaxy/software/tool-data/gatk " -SAMPLES=" -config/galaxy.ini.sample -config/shed_tool_data_table_conf.xml.sample -config/migrated_tools_conf.xml.sample -config/shed_data_manager_conf.xml.sample -tool-data/shared/igv/igv_build_sites.txt.sample -tool-data/shared/rviewer/rviewer_build_sites.txt.sample -tool-data/shared/ucsc/builds.txt.sample -tool-data/shared/ucsc/ucsc_build_sites.txt.sample -" - DIRS=" database database/files @@ -100,11 +89,8 @@ ;; esac -for sample in $SAMPLES; do - file=${sample%.sample} - echo "Copying $sample to $file" - cp $sample $file -done +# set up configs from samples. +./scripts/common_startup.sh echo "Copying job_conf.xml.sample_basic to job_conf.xml" cp config/job_conf.xml.sample_basic config/job_conf.xml https://bitbucket.org/galaxy/galaxy-central/commits/05abe03187a1/ Changeset: 05abe03187a1 User: natefoo Date: 2014-09-23 14:40:50+00:00 Summary: Merge next-stable Affected #: 1 file diff -r 7fcc92fb8035f854b0f72085b40ac5f772ff9205 -r 05abe03187a13527b8da8d0421822090a96969a7 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -42,17 +42,6 @@ /galaxy/software/tool-data/gatk " -SAMPLES=" -config/galaxy.ini.sample -config/shed_tool_data_table_conf.xml.sample -config/migrated_tools_conf.xml.sample -config/shed_data_manager_conf.xml.sample -tool-data/shared/igv/igv_build_sites.txt.sample -tool-data/shared/rviewer/rviewer_build_sites.txt.sample -tool-data/shared/ucsc/builds.txt.sample -tool-data/shared/ucsc/ucsc_build_sites.txt.sample -" - DIRS=" database database/files @@ -100,11 +89,8 @@ ;; esac -for sample in $SAMPLES; do - file=${sample%.sample} - echo "Copying $sample to $file" - cp $sample $file -done +# set up configs from samples. +./scripts/common_startup.sh echo "Copying job_conf.xml.sample_basic to job_conf.xml" cp config/job_conf.xml.sample_basic config/job_conf.xml 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: Merge next-stable to default.
by commits-noreply＠bitbucket.org 23 Sep '14

23 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7fcc92fb8035/ Changeset: 7fcc92fb8035 User: natefoo Date: 2014-09-23 14:12:00+00:00 Summary: Merge next-stable to default. Affected #: 3 files diff -r 5cda4ac27e0a3c7b688e479a593698bfb3f0deb8 -r 7fcc92fb8035f854b0f72085b40ac5f772ff9205 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -13,7 +13,6 @@ import ConfigParser from datetime import timedelta from galaxy.web.formatting import expand_pretty_datetime_format -from galaxy.util.properties import load_app_properties from galaxy.util import string_as_bool from galaxy.util import listify from galaxy.util.dbkeys import GenomeBuilds @@ -37,9 +36,6 @@ deprecated_options = ( 'database_file', ) def __init__( self, **kwargs ): - kwargs = load_app_properties( - kwds=kwargs - ) self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) diff -r 5cda4ac27e0a3c7b688e479a593698bfb3f0deb8 -r 7fcc92fb8035f854b0f72085b40ac5f772ff9205 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -19,6 +19,7 @@ import galaxy.web.framework.webapp from galaxy import util from galaxy.util import asbool +from galaxy.util.properties import load_app_properties import logging log = logging.getLogger( __name__ ) @@ -31,6 +32,9 @@ """ Return a wsgi application serving the root object """ + kwargs = load_app_properties( + kwds=kwargs + ) # Create the Galaxy application unless passed in if 'app' in kwargs: app = kwargs.pop( 'app' ) diff -r 5cda4ac27e0a3c7b688e479a593698bfb3f0deb8 -r 7fcc92fb8035f854b0f72085b40ac5f772ff9205 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -66,8 +66,8 @@ default_galaxy_test_port_max = 9999 default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" -migrated_tool_panel_config = 'migrated_tools_conf.xml' -installed_tool_panel_configs = [ 'shed_tool_conf.xml' ] +migrated_tool_panel_config = 'config/migrated_tools_conf.xml' +installed_tool_panel_configs = [ 'config/shed_tool_conf.xml' ] # should this serve static resources (scripts, images, styles, etc.) STATIC_ENABLED = True @@ -224,7 +224,7 @@ datatypes_conf_override = os.path.join( framework_tool_dir, 'sample_datatypes_conf.xml' ) else: # Use tool_conf.xml toolbox. - tool_conf = 'tool_conf.xml' + tool_conf = None if __check_arg( '-with_framework_test_tools' ): # Some of these tools will not work without swapping # default interactor to point to test. @@ -239,11 +239,10 @@ ignore_files = () start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ + tool_data_table_config_path = None if os.path.exists( 'tool_data_table_conf.test.xml' ): tool_data_table_config_path = 'tool_data_table_conf.test.xml' - else: - tool_data_table_config_path = 'tool_data_table_conf.xml' - shed_tool_data_table_config = 'shed_tool_data_table_conf.xml' + shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False ) galaxy_test_tmp_dir = os.environ.get( 'GALAXY_TEST_TMP_DIR', 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: natefoo: Functional test fix for config file moves.
by commits-noreply＠bitbucket.org 23 Sep '14

23 Sep '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9a05d1ec6f5f/ Changeset: 9a05d1ec6f5f Branch: next-stable User: natefoo Date: 2014-09-23 14:09:17+00:00 Summary: Functional test fix for config file moves. Affected #: 1 file diff -r f721ff18d976e2876648310d59cb6b8c4f6f258b -r 9a05d1ec6f5fb6f95a4c46e14f042b797a13897e scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -66,8 +66,8 @@ default_galaxy_test_port_max = 9999 default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" -migrated_tool_panel_config = 'migrated_tools_conf.xml' -installed_tool_panel_configs = [ 'shed_tool_conf.xml' ] +migrated_tool_panel_config = 'config/migrated_tools_conf.xml' +installed_tool_panel_configs = [ 'config/shed_tool_conf.xml' ] # should this serve static resources (scripts, images, styles, etc.) STATIC_ENABLED = True @@ -224,7 +224,7 @@ datatypes_conf_override = os.path.join( framework_tool_dir, 'sample_datatypes_conf.xml' ) else: # Use tool_conf.xml toolbox. - tool_conf = 'tool_conf.xml' + tool_conf = None if __check_arg( '-with_framework_test_tools' ): # Some of these tools will not work without swapping # default interactor to point to test. @@ -239,11 +239,10 @@ ignore_files = () start_server = 'GALAXY_TEST_EXTERNAL' not in os.environ + tool_data_table_config_path = None if os.path.exists( 'tool_data_table_conf.test.xml' ): tool_data_table_config_path = 'tool_data_table_conf.test.xml' - else: - tool_data_table_config_path = 'tool_data_table_conf.xml' - shed_tool_data_table_config = 'shed_tool_data_table_conf.xml' + shed_tool_data_table_config = 'config/shed_tool_data_table_conf.xml' tool_dependency_dir = os.environ.get( 'GALAXY_TOOL_DEPENDENCY_DIR', None ) use_distributed_object_store = os.environ.get( 'GALAXY_USE_DISTRIBUTED_OBJECT_STORE', False ) galaxy_test_tmp_dir = os.environ.get( 'GALAXY_TEST_TMP_DIR', 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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