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commit/galaxy-central: dannon: Merged in jmchilton/galaxy-central-fork-1 (pull request #558)
by commits-noreply＠bitbucket.org 13 Nov '14

13 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/77676b985228/ Changeset: 77676b985228 User: dannon Date: 2014-11-13 17:18:32+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #558) Make JSONType columns bigger in MySQL Affected #: 2 files diff -r 7f247bf156dfc7cfa7f764cf9757ae3839f0b72c -r 77676b9852282c0a240ebebb410374b233a1fa36 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -65,6 +65,13 @@ def is_mutable( self ): return True + def load_dialect_impl(self, dialect): + if dialect.name == "mysql": + return dialect.type_descriptor(sqlalchemy.dialects.mysql.MEDIUMBLOB) + else: + return self.impl + + metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" ) } ) diff -r 7f247bf156dfc7cfa7f764cf9757ae3839f0b72c -r 77676b9852282c0a240ebebb410374b233a1fa36 lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py @@ -0,0 +1,58 @@ +""" +Migration script to grow MySQL blobs. +""" + +from sqlalchemy import MetaData + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData() + +BLOB_COLUMNS = [ + ("deferred_job", "params"), + ("extended_metadata", "data"), + ("form_definition", "fields"), + ("form_definition", "layout"), + ("form_values", "content"), + ("history_dataset_association", "metadata"), + ("job", "destination_params"), + ("library_dataset_dataset_association", "metadata"), + ("post_job_action", "action_arguments"), + ("request", "notification"), + ("sample", "workflow"), + ("transfer_job", "params"), + ("workflow_step", "tool_inputs"), + ("workflow_step", "tool_errors"), + ("workflow_step", "position"), + ("workflow_step", "config"), + ("tool_shed_repository", "metadata"), + ("tool_shed_repository", "tool_shed_status"), +] + + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + + if migrate_engine.name != "mysql": + return + + for (table, column) in BLOB_COLUMNS: + cmd = "ALTER TABLE %s MODIFY COLUMN %s MEDIUMBLOB;" % (table, column) + try: + migrate_engine.execute( cmd ) + except Exception as e: + print "Failed to grow column %s.%s" % (table, column) + print str( e ) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + # Ignoring..., changed the datatype so no guarantee these columns weren't + # MEDIUMBLOBs before. 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 13 Nov '14

13 Nov '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a94274cfff4c/ Changeset: a94274cfff4c User: jmchilton Date: 2014-11-12 17:46:43+00:00 Summary: Make JSONType a MEDIUMBLOB instead of a BLOB under mysql. These can have 16 MB of data instead of 65 KB - tool shed repositories have encountered problems with the 65 KB limit - though other columns might as well. Affected #: 1 file diff -r f26c2543ff053b9ff31617bc03f99d505302ecda -r a94274cfff4c79d235347ff2c8ebcbd2f10eb96c lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -65,6 +65,13 @@ def is_mutable( self ): return True + def load_dialect_impl(self, dialect): + if dialect.name == "mysql": + return dialect.type_descriptor(sqlalchemy.dialects.mysql.MEDIUMBLOB) + else: + return self.impl + + metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" ) } ) https://bitbucket.org/galaxy/galaxy-central/commits/6b5cd9839533/ Changeset: 6b5cd9839533 User: jmchilton Date: 2014-11-12 17:46:43+00:00 Summary: Database migration to grow mysql blobs. Should address the following issues https://trello.com/c/RbW6pOd2 https://trello.com/c/lvz4OQR1 https://trello.com/c/Hv5iIweU Affected #: 1 file diff -r a94274cfff4c79d235347ff2c8ebcbd2f10eb96c -r 6b5cd9839533db4365ae8cc51a19c37dbe4c2a08 lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py @@ -0,0 +1,58 @@ +""" +Migration script to grow MySQL blobs. +""" + +from sqlalchemy import MetaData + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData() + +BLOB_COLUMNS = [ + ("deferred_job", "params"), + ("extended_metadata", "data"), + ("form_definition", "fields"), + ("form_definition", "layout"), + ("form_values", "content"), + ("history_dataset_association", "metadata"), + ("job", "destination_params"), + ("library_dataset_dataset_association", "metadata"), + ("post_job_action", "action_arguments"), + ("request", "notification"), + ("sample", "workflow"), + ("transfer_job", "params"), + ("workflow_step", "tool_inputs"), + ("workflow_step", "tool_errors"), + ("workflow_step", "position"), + ("workflow_step", "config"), + ("tool_shed_repository", "metadata"), + ("tool_shed_repository", "tool_shed_status"), +] + + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + + if migrate_engine.name != "mysql": + return + + for (table, column) in BLOB_COLUMNS: + cmd = "ALTER TABLE %s MODIFY COLUMN %s MEDIUMBLOB;" % (table, column) + try: + migrate_engine.execute( cmd ) + except Exception as e: + print "Failed to grow column %s.%s" % (table, column) + print str( e ) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + # Ignoring..., changed the datatype so no guarantee these columns weren't + # MEDIUMBLOBs before. https://bitbucket.org/galaxy/galaxy-central/commits/77676b985228/ Changeset: 77676b985228 User: dannon Date: 2014-11-13 17:18:32+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #558) Make JSONType columns bigger in MySQL Affected #: 2 files diff -r 7f247bf156dfc7cfa7f764cf9757ae3839f0b72c -r 77676b9852282c0a240ebebb410374b233a1fa36 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -65,6 +65,13 @@ def is_mutable( self ): return True + def load_dialect_impl(self, dialect): + if dialect.name == "mysql": + return dialect.type_descriptor(sqlalchemy.dialects.mysql.MEDIUMBLOB) + else: + return self.impl + + metadata_pickler = AliasPickleModule( { ( "cookbook.patterns", "Bunch" ) : ( "galaxy.util.bunch" , "Bunch" ) } ) diff -r 7f247bf156dfc7cfa7f764cf9757ae3839f0b72c -r 77676b9852282c0a240ebebb410374b233a1fa36 lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0122_grow_mysql_blobs.py @@ -0,0 +1,58 @@ +""" +Migration script to grow MySQL blobs. +""" + +from sqlalchemy import MetaData + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData() + +BLOB_COLUMNS = [ + ("deferred_job", "params"), + ("extended_metadata", "data"), + ("form_definition", "fields"), + ("form_definition", "layout"), + ("form_values", "content"), + ("history_dataset_association", "metadata"), + ("job", "destination_params"), + ("library_dataset_dataset_association", "metadata"), + ("post_job_action", "action_arguments"), + ("request", "notification"), + ("sample", "workflow"), + ("transfer_job", "params"), + ("workflow_step", "tool_inputs"), + ("workflow_step", "tool_errors"), + ("workflow_step", "position"), + ("workflow_step", "config"), + ("tool_shed_repository", "metadata"), + ("tool_shed_repository", "tool_shed_status"), +] + + +def upgrade(migrate_engine): + metadata.bind = migrate_engine + print __doc__ + metadata.reflect() + + if migrate_engine.name != "mysql": + return + + for (table, column) in BLOB_COLUMNS: + cmd = "ALTER TABLE %s MODIFY COLUMN %s MEDIUMBLOB;" % (table, column) + try: + migrate_engine.execute( cmd ) + except Exception as e: + print "Failed to grow column %s.%s" % (table, column) + print str( e ) + + +def downgrade(migrate_engine): + metadata.bind = migrate_engine + metadata.reflect() + # Ignoring..., changed the datatype so no guarantee these columns weren't + # MEDIUMBLOBs before. 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: fix dataset count off by one error
by commits-noreply＠bitbucket.org 13 Nov '14

13 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7f247bf156df/ Changeset: 7f247bf156df User: carlfeberhard Date: 2014-11-13 16:52:21+00:00 Summary: History panel: fix dataset count off by one error Affected #: 3 files diff -r e802fed907e5341d2d50c94d546a65faf3978a1a -r 7f247bf156dfc7cfa7f764cf9757ae3839f0b72c 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 @@ -354,20 +354,20 @@ * @param {Model} the item model to check */ _handleHdaDeletionChange : function( itemModel ){ - this._renderCounts(); if( itemModel.get( 'deleted' ) && !this.showDeleted ){ this.removeItemView( itemModel ); } + this._renderCounts(); }, /** If this item is hidden and we're not showing hidden items, remove the view * @param {Model} the item model to check */ _handleHdaVisibleChange : function( itemModel ){ - this._renderCounts(); if( itemModel.hidden() && !this.storage.showHidden ){ this.removeItemView( itemModel ); } + this._renderCounts(); }, /** toggle the visibility of each content's tagsEditor applying all the args sent to this function */ diff -r e802fed907e5341d2d50c94d546a65faf3978a1a -r 7f247bf156dfc7cfa7f764cf9757ae3839f0b72c 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 @@ -354,20 +354,20 @@ * @param {Model} the item model to check */ _handleHdaDeletionChange : function( itemModel ){ - this._renderCounts(); if( itemModel.get( 'deleted' ) && !this.showDeleted ){ this.removeItemView( itemModel ); } + this._renderCounts(); }, /** If this item is hidden and we're not showing hidden items, remove the view * @param {Model} the item model to check */ _handleHdaVisibleChange : function( itemModel ){ - this._renderCounts(); if( itemModel.hidden() && !this.storage.showHidden ){ this.removeItemView( itemModel ); } + this._renderCounts(); }, /** toggle the visibility of each content's tagsEditor applying all the args sent to this function */ diff -r e802fed907e5341d2d50c94d546a65faf3978a1a -r 7f247bf156dfc7cfa7f764cf9757ae3839f0b72c 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()},_setUpListeners:function(){i.prototype._setUpListeners.call(this);this.on("drop",function(l,m){this.dataDropped(m);this.dropTargetOff()})},_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},renderItems:function(m){var l=i.prototype.renderItems.call(this,m);this._renderCounts(m);return l},_renderCounts:function(n){function m(q,r){return['<a class="',q,'" href="javascript:void(0);">',r,"</a>"].join("")}n=n||this.$el;var l=this.collection.where({deleted:true}),p=this.collection.where({visible:false}),o=[];if(this.views.length){o.push([this.views.length,b("shown")].join(" "))}if(l.length){o.push((!this.showDeleted)?([l.length,m("toggle-deleted-link",b("deleted"))].join(" ")):(m("toggle-deleted-link",b("hide deleted"))))}if(p.length){o.push((!this.showHidden)?([p.length,m("toggle-hidden-link",b("hidden"))].join(" ")):(m("toggle-hidden-link",b("hide hidden"))))}return n.find("> .controls .subtitle").html(o.join(", "))},_renderTags:function(l){var m=this;this.tagsEditor=new j.TagsEditor({model:this.model,el:l.find(".controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){m.toggleHDATagEditors(true,m.fxSpeed)},onhide:function(){m.toggleHDATagEditors(false,m.fxSpeed)},$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){this._renderCounts();if(l.get("deleted")&&!this.showDeleted){this.removeItemView(l)}},_handleHdaVisibleChange:function(l){this._renderCounts();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","click .toggle-deleted-link":function(l){this.toggleShowDeleted()},"click .toggle-hidden-link":function(l){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var m={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var n=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),n]);for(var l in m){if(m.hasOwnProperty(l)){n.on(l,m[l])}}return this},_renderDropTarget:function(){return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(b("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(l){l.preventDefault();l.stopPropagation()},dragleave:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(n){n.preventDefault();n.dataTransfer.dropEffect="move";var l=this,o=n.dataTransfer.getData("text");try{o=JSON.parse(o)}catch(m){this.warn("error parsing JSON from drop:",o)}this.trigger("droptarget:drop",n,o,l);return false},dataDropped:function(m){var l=this;if(_.isObject(m)&&m.model_class==="HistoryDatasetAssociation"&&m.id){return l.model.contents.copy(m.id)}return jQuery.when()},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()},_setUpListeners:function(){i.prototype._setUpListeners.call(this);this.on("drop",function(l,m){this.dataDropped(m);this.dropTargetOff()})},_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},renderItems:function(m){var l=i.prototype.renderItems.call(this,m);this._renderCounts(m);return l},_renderCounts:function(n){function m(q,r){return['<a class="',q,'" href="javascript:void(0);">',r,"</a>"].join("")}n=n||this.$el;var l=this.collection.where({deleted:true}),p=this.collection.where({visible:false}),o=[];if(this.views.length){o.push([this.views.length,b("shown")].join(" "))}if(l.length){o.push((!this.showDeleted)?([l.length,m("toggle-deleted-link",b("deleted"))].join(" ")):(m("toggle-deleted-link",b("hide deleted"))))}if(p.length){o.push((!this.showHidden)?([p.length,m("toggle-hidden-link",b("hidden"))].join(" ")):(m("toggle-hidden-link",b("hide hidden"))))}return n.find("> .controls .subtitle").html(o.join(", "))},_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.$el.slideDown(l.fxSpeed)},_getItemViewOptions:function(m){var l=i.prototype._getItemViewOptions.call(this,m);_.extend(l,{purgeAllowed:this.purgeAllowed,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.hidden),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.hidden)});return l},_handleHdaDeletionChange:function(l){if(l.get("deleted")&&!this.showDeleted){this.removeItemView(l)}this._renderCounts()},_handleHdaVisibleChange:function(l){if(l.hidden()&&!this.storage.showHidden){this.removeItemView(l)}this._renderCounts()},toggleHDATagEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.tagsEditor){n.tagsEditor.toggle.apply(n.tagsEditor,m)}})},toggleHDAAnnotationEditors:function(l){var m=Array.prototype.slice.call(arguments,1);_.each(this.views,function(n){if(n.annotationEditor){n.annotationEditor.toggle.apply(n.annotationEditor,m)}})},events:_.extend(_.clone(i.prototype.events),{"click .show-selectors-btn":"toggleSelectors","click .toggle-deleted-link":function(l){this.toggleShowDeleted()},"click .toggle-hidden-link":function(l){this.toggleShowHidden()}}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},dropTargetOn:function(){if(this.dropTarget){return this}this.dropTarget=true;var m={dragenter:_.bind(this.dragenter,this),dragover:_.bind(this.dragover,this),dragleave:_.bind(this.dragleave,this),drop:_.bind(this.drop,this)};var n=this._renderDropTarget();this.$list().before([this._renderDropTargetHelp(),n]);for(var l in m){if(m.hasOwnProperty(l)){n.on(l,m[l])}}return this},_renderDropTarget:function(){return $("<div/>").addClass("history-drop-target").css({height:"64px",margin:"0px 10px 10px 10px",border:"1px dashed black","border-radius":"3px"})},_renderDropTargetHelp:function(){return $("<div/>").addClass("history-drop-target-help").css({margin:"10px 10px 4px 10px",color:"grey","font-size":"80%","font-style":"italic"}).text(b("Drag datasets here to copy them to the current history"))},dropTargetOff:function(){if(!this.dropTarget){return this}this.dropTarget=false;this.$(".history-drop-target").remove();this.$(".history-drop-target-help").remove();return this},dropTargetToggle:function(){if(this.dropTarget){this.dropTargetOff()}else{this.dropTargetOn()}return this},dragenter:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","2px solid black")},dragover:function(l){l.preventDefault();l.stopPropagation()},dragleave:function(l){l.preventDefault();l.stopPropagation();this.$(".history-drop-target").css("border","1px dashed black")},drop:function(n){n.preventDefault();n.dataTransfer.dropEffect="move";var l=this,o=n.dataTransfer.getData("text");try{o=JSON.parse(o)}catch(m){this.warn("error parsing JSON from drop:",o)}this.trigger("droptarget:drop",n,o,l);return false},dataDropped:function(m){var l=this;if(_.isObject(m)&&m.model_class==="HistoryDatasetAssociation"&&m.id){return l.model.contents.copy(m.id)}return jQuery.when()},toString:function(){return"HistoryPanelEdit("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanelEdit: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.

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commit/galaxy-central: carlfeberhard: Phyloviz: fix saving
by commits-noreply＠bitbucket.org 13 Nov '14

13 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e802fed907e5/ Changeset: e802fed907e5 User: carlfeberhard Date: 2014-11-13 16:23:12+00:00 Summary: Phyloviz: fix saving Affected #: 3 files diff -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a -r e802fed907e5341d2d50c94d546a65faf3978a1a client/galaxy/scripts/viz/phyloviz.js --- a/client/galaxy/scripts/viz/phyloviz.js +++ b/client/galaxy/scripts/viz/phyloviz.js @@ -199,6 +199,7 @@ this.set("dataset", new data_mod.Dataset({ id: options.dataset_id })); + }, root : {}, // Root has to be its own independent object because it is not part of the viz_config @@ -267,16 +268,14 @@ show_message("Saving to Galaxy", "progress"); return $.ajax({ - url : this.url, + url : this.url(), type : "POST", dataType: "json", data : { - vis_json: JSON.stringify(config) + config : JSON.stringify( config ), + type : 'phyloviz' }, success: function(res){ - var viz_id = res.url.split("id=")[1].split("&")[0], - viz_url = "/visualization?id=" + viz_id; - window.history.pushState({}, "", viz_url + window.location.hash); hide_modal(); } }); diff -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a -r e802fed907e5341d2d50c94d546a65faf3978a1a static/scripts/packed/viz/phyloviz.js --- a/static/scripts/packed/viz/phyloviz.js +++ b/static/scripts/packed/viz/phyloviz.js @@ -1,1 +1,1 @@ -define(["libs/d3","viz/visualization","mvc/data"],function(m,f,g){var l=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(q,o,n){var r=q.val(),s=q.attr("displayLabel")||q.attr("id").replace("phyloViz","");function p(t){return !isNaN(parseFloat(t))&&isFinite(t)}if(!p(r)){alert(s+" is not a number!");return false}if(r>n){alert(s+" is too large.");return false}else{if(r<o){alert(s+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(n){if(n.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). ");return true}return false}});function h(){var w=this,r=m.layout.hierarchy().sort(null).value(null),v=360,q="Linear",u=18,s=200,t=0,p=0.5,n=50;w.leafHeight=function(x){if(typeof x==="undefined"){return u}else{u=x;return w}};w.layoutMode=function(x){if(typeof x==="undefined"){return q}else{q=x;return w}};w.layoutAngle=function(x){if(typeof x==="undefined"){return v}if(isNaN(x)||x<0||x>360){return w}else{v=x;return w}};w.separation=function(x){if(typeof x==="undefined"){return s}else{s=x;return w}};w.links=function(x){return m.layout.tree().links(x)};w.nodes=function(A,y){if(toString.call(A)==="[object Array]"){A=A[0]}var z=r.call(w,A,y),x=[],C=0,B=0;window._d=A;window._nodes=z;z.forEach(function(D){C=D.depth>C?D.depth:C;x.push(D)});x.forEach(function(D){if(!D.children){B+=1;D.depth=C}});u=q==="Circular"?v/B:u;t=0;o(x[0],C,u,null);return x};function o(B,D,A,z){var y=B.children,x=0;var C=B.dist||p;C=C>1?1:C;B.dist=C;if(z!==null){B.y0=z.y0+C*s}else{B.y0=n}if(!y){B.x0=t*A;t+=1}else{y.forEach(function(E){E.parent=B;x+=o(E,D,A,B)});B.x0=x/y.length}B.x=B.x0;B.y=B.y0;return B.x0}return w}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},initialize:function(n){this.set("dataset",new g.Dataset({id:n.dataset_id}))},root:{},toggle:function(n){if(typeof n==="undefined"){return}if(n.children){n._children=n.children;n.children=null}else{n.children=n._children;n._children=null}},toggleAll:function(n){if(n.children&&n.children.length!==0){n.children.forEach(this.toggleAll);toggle(n)}},getData:function(){return this.root},save:function(){var n=this.root;o(n);function o(q){delete q.parent;if(q._selected){delete q._selected}if(q.children){q.children.forEach(o)}if(q._children){q._children.forEach(o)}}var p=jQuery.extend(true,{},this.attributes);p.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url,type:"POST",dataType:"json",data:{vis_json:JSON.stringify(p)},success:function(q){var r=q.url.split("id=")[1].split("&")[0],s="/visualization?id="+r;window.history.pushState({},"",s+window.location.hash);hide_modal()}})}});var d=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(o){var n=this;n.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",n.updateAndRender,n);n.vis=o.vis;n.i=0;n.maxDepth=-1;n.width=o.width;n.height=o.height},updateAndRender:function(p){var o=m.select(".vis"),n=this;p=p||n.model.root;n.renderNodes(p);n.renderLinks(p);n.addTooltips()},renderLinks:function(n){var w=this;var o=w.diagonal;var p=w.duration;var r=w.layoutMode;var t=w.vis.selectAll("g.completeLink").data(w.tree.links(w.nodes),function(x){return x.target.id});var v=function(x){x.pos0=x.source.y0+" "+x.source.x0;x.pos1=x.source.y0+" "+x.target.x0;x.pos2=x.target.y0+" "+x.target.x0};var u=t.enter().insert("svg:g","g.node").attr("class","completeLink");u.append("svg:path").attr("class","link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1});var s=t.transition().duration(500);s.select("path.link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1+" L "+x.pos2});var q=t.exit().remove()},selectNode:function(o){var n=this;m.selectAll("g.node").classed("selectedHighlight",function(p){if(o.id===p.id){if(o._selected){delete o._selected;return false}else{o._selected=true;return true}}return false});n.model.set("selectedNode",o);$("#phyloVizSelectedNodeName").val(o.name);$("#phyloVizSelectedNodeDist").val(o.dist);$("#phyloVizSelectedNodeAnnotation").val(o.annotation||"")},addTooltips:function(){$(".tooltip").remove();$(".node").attr("data-original-title",function(){var o=this.__data__,n=o.annotation||"None";return o?(o.name?o.name+"<br/>":"")+"Dist: "+o.dist+" <br/>Annotation: "+n:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(o){var n=this;n.margins=o.margins;n.layoutMode="Linear";n.stdInit(o);n.layout();n.updateAndRender(n.model.root)},layout:function(){var n=this;n.tree=new h().layoutMode("Linear");n.diagonal=m.svg.diagonal().projection(function(o){return[o.y,o.x]})},renderNodes:function(n){var u=this,v=u.model.get("fontSize")+"px";u.tree.separation(u.model.get("separation")).leafHeight(u.model.get("leafHeight"));var q=500,o=u.tree.separation(u.model.get("separation")).nodes(u.model.root);var p=u.vis.selectAll("g.node").data(o,function(w){return w.name+w.id||(w.id=++u.i)});u.nodes=o;u.duration=q;var r=p.enter().append("svg:g").attr("class","node").on("dblclick",function(){m.event.stopPropagation()}).on("click",function(w){if(m.event.altKey){u.selectNode(w)}else{if(w.children&&w.children.length===0){return}u.model.toggle(w);u.updateAndRender(w)}});if(toString.call(n)==="[object Array]"){n=n[0]}r.attr("transform",function(w){return"translate("+n.y0+","+n.x0+")"});r.append("svg:circle").attr("r",0.000001).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});r.append("svg:text").attr("class","nodeLabel").attr("x",function(w){return w.children||w._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(w){return w.children||w._children?"end":"start"}).style("fill-opacity",0.000001);var s=p.transition().duration(q);s.attr("transform",function(w){return"translate("+w.y+","+w.x+")"});s.select("circle").attr("r",u.defaults.nodeRadius).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});s.select("text").style("fill-opacity",1).style("font-size",v).text(function(w){return w.name});var t=p.exit().transition().duration(q).remove();t.select("circle").attr("r",0.000001);t.select("text").style("fill-opacity",0.000001);o.forEach(function(w){w.x0=w.x;w.y0=w.y})}});var j=Backbone.View.extend({className:"phyloviz",initialize:function(o){var n=this;n.MIN_SCALE=0.05;n.MAX_SCALE=5;n.MAX_DISPLACEMENT=500;n.margins=[10,60,10,80];n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.radius=n.width;n.data=o.data;$(window).resize(function(){n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.render()});n.phyloTree=new b(o.config);n.phyloTree.root=n.data;n.zoomFunc=m.behavior.zoom().scaleExtent([n.MIN_SCALE,n.MAX_SCALE]);n.zoomFunc.translate(n.phyloTree.get("translate"));n.zoomFunc.scale(n.phyloTree.get("scaleFactor"));n.navMenu=new c(n);n.settingsMenu=new i({phyloTree:n.phyloTree});n.nodeSelectionView=new e({phyloTree:n.phyloTree});n.search=new k();setTimeout(function(){n.zoomAndPan()},1000)},render:function(){var o=this;$("#PhyloViz").empty();o.mainSVG=m.select("#PhyloViz").append("svg:svg").attr("width",o.width).attr("height",o.height).attr("pointer-events","all").call(o.zoomFunc.on("zoom",function(){o.zoomAndPan()}));o.boundingRect=o.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",o.width).attr("height",o.height).attr("stroke","black").attr("fill","white");o.vis=o.mainSVG.append("svg:g").attr("class","vis");o.layoutOptions={model:o.phyloTree,width:o.width,height:o.height,vis:o.vis,margins:o.margins};$("#title").text("Phylogenetic Tree from "+o.phyloTree.get("title")+":");var n=new a(o.layoutOptions)},zoomAndPan:function(n){var t,p;if(typeof n!=="undefined"){t=n.zoom;p=n.translate}var w=this,r=w.zoomFunc.scale(),v=w.zoomFunc.translate(),s="",u="";switch(t){case"reset":r=1;v=[0,0];break;case"+":r*=1.1;break;case"-":r*=0.9;break;default:if(typeof t==="number"){r=t}else{if(m.event!==null){r=m.event.scale}}}if(r<w.MIN_SCALE||r>w.MAX_SCALE){return}w.zoomFunc.scale(r);s="translate("+w.margins[3]+","+w.margins[0]+") scale("+r+")";if(m.event!==null){u="translate("+m.event.translate+")"}else{if(typeof p!=="undefined"){var q=p.split(",")[0];var o=p.split(",")[1];if(!isNaN(q)&&!isNaN(o)){v=[v[0]+parseFloat(q),v[1]+parseFloat(o)]}}w.zoomFunc.translate(v);u="translate("+v+")"}w.phyloTree.set("scaleFactor",r);w.phyloTree.set("translate",v);w.vis.attr("transform",u+s)},reloadViz:function(){var n=this,o=$("#phylovizNexSelector :selected").val();$.getJSON(n.phyloTree.get("dataset").url(),{tree_index:o,data_type:"raw_data"},function(p){n.data=p.data;n.config=p;n.render()})}});var c=Backbone.View.extend({initialize:function(o){var n=this;n.phylovizView=o;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();n.initNavBtns();n.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){n.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var n=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();n.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var o=$("#phylovizNexSelector option:selected").text();if(o){n.phylovizView.phyloTree.set("title",o)}n.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("https://wiki.galaxyproject.org/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var n=this,o=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){n.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){n.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){n.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(o.$el)}});var i=l.extend({className:"Settings",initialize:function(o){var n=this;n.phyloTree=o.phyloTree;n.el=$("#SettingsMenu");n.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){n.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){n.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){n.apply()})},apply:function(){var n=this;if(!n.isAcceptableValue(n.inputs.separation,50,2500)||!n.isAcceptableValue(n.inputs.leafHeight,5,30)||!n.isAcceptableValue(n.inputs.fontSize,5,20)){return}$.each(n.inputs,function(o,p){n.phyloTree.set(o,p.val())})},updateUI:function(){var n=this;$.each(n.inputs,function(o,p){p.val(n.phyloTree.get(o))})},resetToDefaults:function(){$(".tooltip").remove();var n=this;$.each(n.phyloTree.defaults,function(o,p){n.phyloTree.set(o,p)});n.updateUI()},render:function(){}});var e=l.extend({className:"Settings",initialize:function(o){var n=this;n.el=$("#nodeSelectionView");n.phyloTree=o.phyloTree;n.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};n.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){n.el.hide()});n.UI.saveChanges.off().on("click",function(){n.updateNodes()});n.UI.cancelChanges.off().on("click",function(){n.cancelChanges()});(function(p){p.fn.enable=function(q){return p(this).each(function(){if(q){p(this).removeAttr("disabled")}else{p(this).attr("disabled","disabled")}})}})(jQuery);n.UI.enableEdit.off().on("click",function(){n.toggleUI()})},toggleUI:function(){var n=this,o=n.UI.enableEdit.is(":checked");if(!o){n.cancelChanges()}$.each(n.valuesOfConcern,function(p,q){n.UI[p].enable(o)});if(o){n.UI.saveChanges.show();n.UI.cancelChanges.show()}else{n.UI.saveChanges.hide();n.UI.cancelChanges.hide()}},cancelChanges:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){$.each(n.valuesOfConcern,function(p,q){n.UI[p].val(o[p])})}},updateNodes:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){if(!n.isAcceptableValue(n.UI.dist,0,1)||n.hasIllegalJsonCharacters(n.UI.name)||n.hasIllegalJsonCharacters(n.UI.annotation)){return}$.each(n.valuesOfConcern,function(p,q){(o[p])=n.UI[p].val()});n.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var k=l.extend({initialize:function(){var n=this;$("#phyloVizSearchBtn").on("click",function(){var p=$("#phyloVizSearchTerm"),q=$("#phyloVizSearchCondition").val().split("-"),o=q[0],r=q[1];n.hasIllegalJsonCharacters(p);if(o==="dist"){n.isAcceptableValue(p,0,1)}n.searchTree(o,r,p.val())})},searchTree:function(n,p,o){m.selectAll("g.node").classed("searchHighlight",function(r){var q=r[n];if(typeof q!=="undefined"&&q!==null){if(n==="dist"){switch(p){case"greaterEqual":return q>=+o;case"lesserEqual":return q<=+o;default:return}}else{if(n==="name"||n==="annotation"){return q.toLowerCase().indexOf(o.toLowerCase())!==-1}}}})}});return{PhylovizView:j}}); \ No newline at end of file +define(["libs/d3","viz/visualization","mvc/data"],function(m,f,g){var l=Backbone.View.extend({className:"UserMenuBase",isAcceptableValue:function(q,o,n){var r=q.val(),s=q.attr("displayLabel")||q.attr("id").replace("phyloViz","");function p(t){return !isNaN(parseFloat(t))&&isFinite(t)}if(!p(r)){alert(s+" is not a number!");return false}if(r>n){alert(s+" is too large.");return false}else{if(r<o){alert(s+" is too small.");return false}}return true},hasIllegalJsonCharacters:function(n){if(n.val().search(/"|'|\\/)!==-1){alert("Named fields cannot contain these illegal characters: double quote(\"), single guote('), or back slash(\\). ");return true}return false}});function h(){var w=this,r=m.layout.hierarchy().sort(null).value(null),v=360,q="Linear",u=18,s=200,t=0,p=0.5,n=50;w.leafHeight=function(x){if(typeof x==="undefined"){return u}else{u=x;return w}};w.layoutMode=function(x){if(typeof x==="undefined"){return q}else{q=x;return w}};w.layoutAngle=function(x){if(typeof x==="undefined"){return v}if(isNaN(x)||x<0||x>360){return w}else{v=x;return w}};w.separation=function(x){if(typeof x==="undefined"){return s}else{s=x;return w}};w.links=function(x){return m.layout.tree().links(x)};w.nodes=function(A,y){if(toString.call(A)==="[object Array]"){A=A[0]}var z=r.call(w,A,y),x=[],C=0,B=0;window._d=A;window._nodes=z;z.forEach(function(D){C=D.depth>C?D.depth:C;x.push(D)});x.forEach(function(D){if(!D.children){B+=1;D.depth=C}});u=q==="Circular"?v/B:u;t=0;o(x[0],C,u,null);return x};function o(B,D,A,z){var y=B.children,x=0;var C=B.dist||p;C=C>1?1:C;B.dist=C;if(z!==null){B.y0=z.y0+C*s}else{B.y0=n}if(!y){B.x0=t*A;t+=1}else{y.forEach(function(E){E.parent=B;x+=o(E,D,A,B)});B.x0=x/y.length}B.x=B.x0;B.y=B.y0;return B.x0}return w}var b=f.Visualization.extend({defaults:{layout:"Linear",separation:250,leafHeight:18,type:"phyloviz",title:"Title",scaleFactor:1,translate:[0,0],fontSize:12,selectedNode:null,nodeAttrChangedTime:0},initialize:function(n){this.set("dataset",new g.Dataset({id:n.dataset_id}))},root:{},toggle:function(n){if(typeof n==="undefined"){return}if(n.children){n._children=n.children;n.children=null}else{n.children=n._children;n._children=null}},toggleAll:function(n){if(n.children&&n.children.length!==0){n.children.forEach(this.toggleAll);toggle(n)}},getData:function(){return this.root},save:function(){var n=this.root;o(n);function o(q){delete q.parent;if(q._selected){delete q._selected}if(q.children){q.children.forEach(o)}if(q._children){q._children.forEach(o)}}var p=jQuery.extend(true,{},this.attributes);p.selectedNode=null;show_message("Saving to Galaxy","progress");return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{config:JSON.stringify(p),type:"phyloviz"},success:function(q){hide_modal()}})}});var d=Backbone.View.extend({defaults:{nodeRadius:4.5},stdInit:function(o){var n=this;n.model.on("change:separation change:leafHeight change:fontSize change:nodeAttrChangedTime",n.updateAndRender,n);n.vis=o.vis;n.i=0;n.maxDepth=-1;n.width=o.width;n.height=o.height},updateAndRender:function(p){var o=m.select(".vis"),n=this;p=p||n.model.root;n.renderNodes(p);n.renderLinks(p);n.addTooltips()},renderLinks:function(n){var w=this;var o=w.diagonal;var p=w.duration;var r=w.layoutMode;var t=w.vis.selectAll("g.completeLink").data(w.tree.links(w.nodes),function(x){return x.target.id});var v=function(x){x.pos0=x.source.y0+" "+x.source.x0;x.pos1=x.source.y0+" "+x.target.x0;x.pos2=x.target.y0+" "+x.target.x0};var u=t.enter().insert("svg:g","g.node").attr("class","completeLink");u.append("svg:path").attr("class","link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1});var s=t.transition().duration(500);s.select("path.link").attr("d",function(x){v(x);return"M "+x.pos0+" L "+x.pos1+" L "+x.pos2});var q=t.exit().remove()},selectNode:function(o){var n=this;m.selectAll("g.node").classed("selectedHighlight",function(p){if(o.id===p.id){if(o._selected){delete o._selected;return false}else{o._selected=true;return true}}return false});n.model.set("selectedNode",o);$("#phyloVizSelectedNodeName").val(o.name);$("#phyloVizSelectedNodeDist").val(o.dist);$("#phyloVizSelectedNodeAnnotation").val(o.annotation||"")},addTooltips:function(){$(".tooltip").remove();$(".node").attr("data-original-title",function(){var o=this.__data__,n=o.annotation||"None";return o?(o.name?o.name+"<br/>":"")+"Dist: "+o.dist+" <br/>Annotation: "+n:""}).tooltip({placement:"top",trigger:"hover"})}});var a=d.extend({initialize:function(o){var n=this;n.margins=o.margins;n.layoutMode="Linear";n.stdInit(o);n.layout();n.updateAndRender(n.model.root)},layout:function(){var n=this;n.tree=new h().layoutMode("Linear");n.diagonal=m.svg.diagonal().projection(function(o){return[o.y,o.x]})},renderNodes:function(n){var u=this,v=u.model.get("fontSize")+"px";u.tree.separation(u.model.get("separation")).leafHeight(u.model.get("leafHeight"));var q=500,o=u.tree.separation(u.model.get("separation")).nodes(u.model.root);var p=u.vis.selectAll("g.node").data(o,function(w){return w.name+w.id||(w.id=++u.i)});u.nodes=o;u.duration=q;var r=p.enter().append("svg:g").attr("class","node").on("dblclick",function(){m.event.stopPropagation()}).on("click",function(w){if(m.event.altKey){u.selectNode(w)}else{if(w.children&&w.children.length===0){return}u.model.toggle(w);u.updateAndRender(w)}});if(toString.call(n)==="[object Array]"){n=n[0]}r.attr("transform",function(w){return"translate("+n.y0+","+n.x0+")"});r.append("svg:circle").attr("r",0.000001).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});r.append("svg:text").attr("class","nodeLabel").attr("x",function(w){return w.children||w._children?-10:10}).attr("dy",".35em").attr("text-anchor",function(w){return w.children||w._children?"end":"start"}).style("fill-opacity",0.000001);var s=p.transition().duration(q);s.attr("transform",function(w){return"translate("+w.y+","+w.x+")"});s.select("circle").attr("r",u.defaults.nodeRadius).style("fill",function(w){return w._children?"lightsteelblue":"#fff"});s.select("text").style("fill-opacity",1).style("font-size",v).text(function(w){return w.name});var t=p.exit().transition().duration(q).remove();t.select("circle").attr("r",0.000001);t.select("text").style("fill-opacity",0.000001);o.forEach(function(w){w.x0=w.x;w.y0=w.y})}});var j=Backbone.View.extend({className:"phyloviz",initialize:function(o){var n=this;n.MIN_SCALE=0.05;n.MAX_SCALE=5;n.MAX_DISPLACEMENT=500;n.margins=[10,60,10,80];n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.radius=n.width;n.data=o.data;$(window).resize(function(){n.width=$("#PhyloViz").width();n.height=$("#PhyloViz").height();n.render()});n.phyloTree=new b(o.config);n.phyloTree.root=n.data;n.zoomFunc=m.behavior.zoom().scaleExtent([n.MIN_SCALE,n.MAX_SCALE]);n.zoomFunc.translate(n.phyloTree.get("translate"));n.zoomFunc.scale(n.phyloTree.get("scaleFactor"));n.navMenu=new c(n);n.settingsMenu=new i({phyloTree:n.phyloTree});n.nodeSelectionView=new e({phyloTree:n.phyloTree});n.search=new k();setTimeout(function(){n.zoomAndPan()},1000)},render:function(){var o=this;$("#PhyloViz").empty();o.mainSVG=m.select("#PhyloViz").append("svg:svg").attr("width",o.width).attr("height",o.height).attr("pointer-events","all").call(o.zoomFunc.on("zoom",function(){o.zoomAndPan()}));o.boundingRect=o.mainSVG.append("svg:rect").attr("class","boundingRect").attr("width",o.width).attr("height",o.height).attr("stroke","black").attr("fill","white");o.vis=o.mainSVG.append("svg:g").attr("class","vis");o.layoutOptions={model:o.phyloTree,width:o.width,height:o.height,vis:o.vis,margins:o.margins};$("#title").text("Phylogenetic Tree from "+o.phyloTree.get("title")+":");var n=new a(o.layoutOptions)},zoomAndPan:function(n){var t,p;if(typeof n!=="undefined"){t=n.zoom;p=n.translate}var w=this,r=w.zoomFunc.scale(),v=w.zoomFunc.translate(),s="",u="";switch(t){case"reset":r=1;v=[0,0];break;case"+":r*=1.1;break;case"-":r*=0.9;break;default:if(typeof t==="number"){r=t}else{if(m.event!==null){r=m.event.scale}}}if(r<w.MIN_SCALE||r>w.MAX_SCALE){return}w.zoomFunc.scale(r);s="translate("+w.margins[3]+","+w.margins[0]+") scale("+r+")";if(m.event!==null){u="translate("+m.event.translate+")"}else{if(typeof p!=="undefined"){var q=p.split(",")[0];var o=p.split(",")[1];if(!isNaN(q)&&!isNaN(o)){v=[v[0]+parseFloat(q),v[1]+parseFloat(o)]}}w.zoomFunc.translate(v);u="translate("+v+")"}w.phyloTree.set("scaleFactor",r);w.phyloTree.set("translate",v);w.vis.attr("transform",u+s)},reloadViz:function(){var n=this,o=$("#phylovizNexSelector :selected").val();$.getJSON(n.phyloTree.get("dataset").url(),{tree_index:o,data_type:"raw_data"},function(p){n.data=p.data;n.config=p;n.render()})}});var c=Backbone.View.extend({initialize:function(o){var n=this;n.phylovizView=o;$("#panelHeaderRightBtns").empty();$("#phyloVizNavBtns").empty();$("#phylovizNexSelector").off();n.initNavBtns();n.initRightHeaderBtns();$("#phylovizNexSelector").off().on("change",function(){n.phylovizView.reloadViz()})},initRightHeaderBtns:function(){var n=this;rightMenu=create_icon_buttons_menu([{icon_class:"gear",title:"PhyloViz Settings",on_click:function(){$("#SettingsMenu").show();n.settingsMenu.updateUI()}},{icon_class:"disk",title:"Save visualization",on_click:function(){var o=$("#phylovizNexSelector option:selected").text();if(o){n.phylovizView.phyloTree.set("title",o)}n.phylovizView.phyloTree.save()}},{icon_class:"chevron-expand",title:"Search / Edit Nodes",on_click:function(){$("#nodeSelectionView").show()}},{icon_class:"information",title:"Phyloviz Help",on_click:function(){window.open("https://wiki.galaxyproject.org/Learn/Visualization/PhylogeneticTree")}}],{tooltip_config:{placement:"bottom"}});$("#panelHeaderRightBtns").append(rightMenu.$el)},initNavBtns:function(){var n=this,o=create_icon_buttons_menu([{icon_class:"zoom-in",title:"Zoom in",on_click:function(){n.phylovizView.zoomAndPan({zoom:"+"})}},{icon_class:"zoom-out",title:"Zoom out",on_click:function(){n.phylovizView.zoomAndPan({zoom:"-"})}},{icon_class:"arrow-circle",title:"Reset Zoom/Pan",on_click:function(){n.phylovizView.zoomAndPan({zoom:"reset"})}}],{tooltip_config:{placement:"bottom"}});$("#phyloVizNavBtns").append(o.$el)}});var i=l.extend({className:"Settings",initialize:function(o){var n=this;n.phyloTree=o.phyloTree;n.el=$("#SettingsMenu");n.inputs={separation:$("#phyloVizTreeSeparation"),leafHeight:$("#phyloVizTreeLeafHeight"),fontSize:$("#phyloVizTreeFontSize")};$("#settingsCloseBtn").off().on("click",function(){n.el.hide()});$("#phylovizResetSettingsBtn").off().on("click",function(){n.resetToDefaults()});$("#phylovizApplySettingsBtn").off().on("click",function(){n.apply()})},apply:function(){var n=this;if(!n.isAcceptableValue(n.inputs.separation,50,2500)||!n.isAcceptableValue(n.inputs.leafHeight,5,30)||!n.isAcceptableValue(n.inputs.fontSize,5,20)){return}$.each(n.inputs,function(o,p){n.phyloTree.set(o,p.val())})},updateUI:function(){var n=this;$.each(n.inputs,function(o,p){p.val(n.phyloTree.get(o))})},resetToDefaults:function(){$(".tooltip").remove();var n=this;$.each(n.phyloTree.defaults,function(o,p){n.phyloTree.set(o,p)});n.updateUI()},render:function(){}});var e=l.extend({className:"Settings",initialize:function(o){var n=this;n.el=$("#nodeSelectionView");n.phyloTree=o.phyloTree;n.UI={enableEdit:$("#phylovizEditNodesCheck"),saveChanges:$("#phylovizNodeSaveChanges"),cancelChanges:$("#phylovizNodeCancelChanges"),name:$("#phyloVizSelectedNodeName"),dist:$("#phyloVizSelectedNodeDist"),annotation:$("#phyloVizSelectedNodeAnnotation")};n.valuesOfConcern={name:null,dist:null,annotation:null};$("#nodeSelCloseBtn").off().on("click",function(){n.el.hide()});n.UI.saveChanges.off().on("click",function(){n.updateNodes()});n.UI.cancelChanges.off().on("click",function(){n.cancelChanges()});(function(p){p.fn.enable=function(q){return p(this).each(function(){if(q){p(this).removeAttr("disabled")}else{p(this).attr("disabled","disabled")}})}})(jQuery);n.UI.enableEdit.off().on("click",function(){n.toggleUI()})},toggleUI:function(){var n=this,o=n.UI.enableEdit.is(":checked");if(!o){n.cancelChanges()}$.each(n.valuesOfConcern,function(p,q){n.UI[p].enable(o)});if(o){n.UI.saveChanges.show();n.UI.cancelChanges.show()}else{n.UI.saveChanges.hide();n.UI.cancelChanges.hide()}},cancelChanges:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){$.each(n.valuesOfConcern,function(p,q){n.UI[p].val(o[p])})}},updateNodes:function(){var n=this,o=n.phyloTree.get("selectedNode");if(o){if(!n.isAcceptableValue(n.UI.dist,0,1)||n.hasIllegalJsonCharacters(n.UI.name)||n.hasIllegalJsonCharacters(n.UI.annotation)){return}$.each(n.valuesOfConcern,function(p,q){(o[p])=n.UI[p].val()});n.phyloTree.set("nodeAttrChangedTime",new Date())}else{alert("No node selected")}}});var k=l.extend({initialize:function(){var n=this;$("#phyloVizSearchBtn").on("click",function(){var p=$("#phyloVizSearchTerm"),q=$("#phyloVizSearchCondition").val().split("-"),o=q[0],r=q[1];n.hasIllegalJsonCharacters(p);if(o==="dist"){n.isAcceptableValue(p,0,1)}n.searchTree(o,r,p.val())})},searchTree:function(n,p,o){m.selectAll("g.node").classed("searchHighlight",function(r){var q=r[n];if(typeof q!=="undefined"&&q!==null){if(n==="dist"){switch(p){case"greaterEqual":return q>=+o;case"lesserEqual":return q<=+o;default:return}}else{if(n==="name"||n==="annotation"){return q.toLowerCase().indexOf(o.toLowerCase())!==-1}}}})}});return{PhylovizView:j}}); \ No newline at end of file diff -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a -r e802fed907e5341d2d50c94d546a65faf3978a1a static/scripts/viz/phyloviz.js --- a/static/scripts/viz/phyloviz.js +++ b/static/scripts/viz/phyloviz.js @@ -199,6 +199,7 @@ this.set("dataset", new data_mod.Dataset({ id: options.dataset_id })); + }, root : {}, // Root has to be its own independent object because it is not part of the viz_config @@ -267,16 +268,14 @@ show_message("Saving to Galaxy", "progress"); return $.ajax({ - url : this.url, + url : this.url(), type : "POST", dataType: "json", data : { - vis_json: JSON.stringify(config) + config : JSON.stringify( config ), + type : 'phyloviz' }, success: function(res){ - var viz_id = res.url.split("id=")[1].split("&")[0], - viz_url = "/visualization?id=" + viz_id; - window.history.pushState({}, "", viz_url + window.location.hash); hide_modal(); } }); 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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[galaxyproject/usegalaxy-playbook] 9e763a: Static memory increases for certain tools.
by GitHub 13 Nov '14

13 Nov '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9e763a5005cb48a34122e78c208607d7aae93783 https://github.com/galaxyproject/usegalaxy-playbook/commit/9e763a5005cb48a3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-13 (Thu, 13 Nov 2014) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Static memory increases for certain tools. Commit: ea2825245643691aa084a51976e19635b97ebe28 https://github.com/galaxyproject/usegalaxy-playbook/commit/ea2825245643691a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-11-13 (Thu, 13 Nov 2014) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M production/group_vars/all.yml M stage/group_vars/all.yml Log Message: ----------- Update Test and Main. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/f1c38cf9ddc8...…

1 0

commit/galaxy-central: guerler: ToolForm: Test tool form width limits
by commits-noreply＠bitbucket.org 13 Nov '14

13 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e372aaa3b3bc/ Changeset: e372aaa3b3bc User: guerler Date: 2014-11-13 14:59:08+00:00 Summary: ToolForm: Test tool form width limits Affected #: 5 files diff -r dfdb4c8c2d12261bdc691ec0db32ad459b0c2525 -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a 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 @@ -334,6 +334,7 @@ this.portlet = new Portlet.View({ icon : 'fa-wrench', title: '<b>' + this.model.name + '</b> ' + this.model.description, + cls : 'ui-portlet-short', operations: { menu : menu }, diff -r dfdb4c8c2d12261bdc691ec0db32ad459b0c2525 -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -334,6 +334,7 @@ this.portlet = new Portlet.View({ icon : 'fa-wrench', title: '<b>' + this.model.name + '</b> ' + this.model.description, + cls : 'ui-portlet-short', operations: { menu : menu }, diff -r dfdb4c8c2d12261bdc691ec0db32ad459b0c2525 -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a 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(["utils/utils","utils/deferred","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-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","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-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-short",operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r dfdb4c8c2d12261bdc691ec0db32ad459b0c2525 -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1279,7 +1279,7 @@ .upload-ftp .upload-ftp-help{margin-bottom:10px} .upload-ftp .upload-ftp-warning{text-align:center;margin-top:20px} .upload-settings .upload-settings-cover{position:absolute;width:100%;height:100%;top:0px;left:0px;background:#fff;opacity:0.4;cursor:no-drop} -.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-repeat{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} +.no-highlight,.ui-button-icon,.ui-portlet,.ui-portlet-short,.ui-portlet-repeat{-webkit-user-select:none;-moz-user-select:none;-khtml-user-select:none;-ms-user-select:none;} .ui-error{-moz-border-radius:3px;border-radius:3px;background:#f9c7c5;padding:5px} .ui-table-form-error{display:none}.ui-table-form-error .ui-table-form-error-text{padding-left:5px} .ui-table tbody{cursor:pointer} @@ -1302,11 +1302,12 @@ .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} -.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,.ui-portlet-short,.ui-portlet-repeat,.ui-portlet-short,.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,.ui-portlet-short .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,.ui-portlet-short .portlet-header .portlet-title .portlet-title-text{vertical-align:middle} +.ui-portlet .portlet-header .portlet-title .icon,.ui-portlet-short .portlet-header .portlet-title .icon{font-size:1.2em;vertical-align:middle} +.ui-portlet .portlet-buttons,.ui-portlet-short .portlet-buttons{height:50px;padding:10px} +.ui-portlet .portlet-content,.ui-portlet-short .portlet-content{height:inherit;padding:10px;clear:both}.ui-portlet .portlet-content .content,.ui-portlet-short .portlet-content .content{padding:10px;height:100%;width:100%}.ui-portlet .portlet-content .content .buttons,.ui-portlet-short .portlet-content .content .buttons{height:50px;padding:10px} +.ui-portlet .no-scroll,.ui-portlet-short .no-scroll{height:calc(100% - 80px)} +.ui-portlet-short .portlet-content{max-width:600px} .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} diff -r dfdb4c8c2d12261bdc691ec0db32ad459b0c2525 -r e372aaa3b3bc1ab9f9b8053d277c678647e8007a static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -200,6 +200,13 @@ } } +.ui-portlet-short { + &:extend(.ui-portlet all); + .portlet-content { + max-width: 600px; + } +} + .ui-portlet-repeat { &:extend(.ui-portlet); border: none; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Fix collection ids
by commits-noreply＠bitbucket.org 12 Nov '14

12 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dfdb4c8c2d12/ Changeset: dfdb4c8c2d12 User: guerler Date: 2014-11-12 20:33:53+00:00 Summary: ToolForm: Fix collection ids Affected #: 1 file diff -r 76ec1e41fe30300ce12c72167ce38990028f6c27 -r dfdb4c8c2d12261bdc691ec0db32ad459b0c2525 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2100,7 +2100,7 @@ if dataset_collection_matcher.hdca_match( hdca, reduction=multiple ): d['options']['hdca'].append({ 'id' : trans.security.encode_id( hdca.id ), - 'id_uncoded' : hda.id, + 'id_uncoded' : hdca.id, 'hid' : hdca.hid, 'name' : hdca.name, 'src' : 'hdca' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Temporary modification of return dictionary for datasets
by commits-noreply＠bitbucket.org 12 Nov '14

12 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/76ec1e41fe30/ Changeset: 76ec1e41fe30 User: guerler Date: 2014-11-12 20:30:35+00:00 Summary: ToolForm: Temporary modification of return dictionary for datasets Affected #: 4 files diff -r 31f05a12912be544f59a85239e584eeac15a4b98 -r 76ec1e41fe30300ce12c72167ce38990028f6c27 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 @@ -148,7 +148,7 @@ var current_state = this.tree.finalize({ data : function(dict) { if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { - return self.content.get({id: dict.values[0].id, src: 'hda'}).dataset_id; + return self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; } return null; } diff -r 31f05a12912be544f59a85239e584eeac15a4b98 -r 76ec1e41fe30300ce12c72167ce38990028f6c27 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2088,10 +2088,10 @@ if dataset_matcher.hda_match( hda ): d['options']['hda'].append({ 'id' : trans.security.encode_id( hda.id ), + 'id_uncoded' : hda.id, 'hid' : hda.hid, 'name' : hda.name, - 'src' : 'hda', - 'dataset_id' : hda.dataset_id + 'src' : 'hda' }) # add dataset collections @@ -2100,6 +2100,7 @@ if dataset_collection_matcher.hdca_match( hdca, reduction=multiple ): d['options']['hdca'].append({ 'id' : trans.security.encode_id( hdca.id ), + 'id_uncoded' : hda.id, 'hid' : hdca.hid, 'name' : hdca.name, 'src' : 'hdca' diff -r 31f05a12912be544f59a85239e584eeac15a4b98 -r 76ec1e41fe30300ce12c72167ce38990028f6c27 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -148,7 +148,7 @@ var current_state = this.tree.finalize({ data : function(dict) { if (dict.values.length > 0 && dict.values[0] && dict.values[0].src === 'hda') { - return self.content.get({id: dict.values[0].id, src: 'hda'}).dataset_id; + return self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; } return null; } diff -r 31f05a12912be544f59a85239e584eeac15a4b98 -r 76ec1e41fe30300ce12c72167ce38990028f6c27 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(["utils/utils","utils/deferred","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-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","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-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Pages: allow registry visualizations to display within an iframe; Refactor embed_item.less and minor style fixes
by commits-noreply＠bitbucket.org 12 Nov '14

12 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/31f05a12912b/ Changeset: 31f05a12912b User: carlfeberhard Date: 2014-11-12 18:45:38+00:00 Summary: Pages: allow registry visualizations to display within an iframe; Refactor embed_item.less and minor style fixes Affected #: 7 files diff -r f26c2543ff053b9ff31617bc03f99d505302ecda -r 31f05a12912be544f59a85239e584eeac15a4b98 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -755,6 +755,28 @@ user_is_owner=user_is_owner, history_dict=history_dictionary, hda_dicts=hda_dictionaries ) return filled + def _get_embedded_visualization_html( self, trans, id ): + """ + Returns html suitable for embedding visualizations in another page. + """ + visualization = self.get_visualization( trans, id, False, True ) + visualization.annotation = self.get_item_annotation_str( trans.sa_session, visualization.user, visualization ) + if not visualization: + return None + + # Fork to template based on visualization.type (registry or builtin). + if( ( trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins ) + and ( visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS ) ): + # if a registry visualization, load a version into an iframe :( + #TODO: simplest path from A to B but not optimal - will be difficult to do reg visualizations any other way + #TODO: this will load the visualization twice (once above, once when the iframe src calls 'saved') + encoded_visualization_id = trans.security.encode_id( visualization.id ) + return trans.fill_template( 'visualization/embed_in_frame.mako', + item=visualization, encoded_visualization_id=encoded_visualization_id, + content_only=True ) + + return trans.fill_template( "visualization/embed.mako", item=visualization, item_data=None ) + def _get_embed_html( self, trans, item_class, item_id ): """ Returns HTML for embedding an item in a page. """ item_class = self.get_class( item_class ) @@ -776,10 +798,7 @@ return trans.fill_template( "workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps ) elif item_class == model.Visualization: - visualization = self.get_visualization( trans, item_id, False, True ) - visualization.annotation = self.get_item_annotation_str( trans.sa_session, visualization.user, visualization ) - if visualization: - return trans.fill_template( "visualization/embed.mako", item=visualization, item_data=None ) + return self._get_embedded_visualization_html( trans, item_id ) elif item_class == model.Page: pass diff -r f26c2543ff053b9ff31617bc03f99d505302ecda -r 31f05a12912be544f59a85239e584eeac15a4b98 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -585,7 +585,7 @@ user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, visualization ) - # Display. + # Fork to template based on visualization.type (registry or builtin). if( ( trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins ) and ( visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS ) ): # if a registry visualization, load a version of display.mako that will load the vis into an iframe :( diff -r f26c2543ff053b9ff31617bc03f99d505302ecda -r 31f05a12912be544f59a85239e584eeac15a4b98 static/style/blue/embed_item.css --- a/static/style/blue/embed_item.css +++ b/static/style/blue/embed_item.css @@ -1,19 +1,14 @@ -.embedded-item{margin:0em auto;width:90%;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em} -.embedded-item.display{padding:5px 10px 10px 10px} -.embedded-item.history{background-color:#c1c9e5} -.embedded-item.history p{background:#c1c9e5 no-repeat 2px 2px;margin-top:0;margin-bottom:0} -.embedded-item.dataset{background-color:#cfc} -.embedded-item.dataset p{background:#cfc no-repeat 2px 2px;margin-top:0;margin-bottom:0} -.embedded-item.workflow{background-color:#fbddb3} -.embedded-item.workflow p{background:#fbddb3 no-repeat 2px 2px;margin-top:0;margin-bottom:0} -.embedded-item.visualization{background-color:#bbb} -.embedded-item.visualization p{background:#bbb no-repeat 2px 2px;margin-top:0;margin-bottom:0} -.embedded-item .expanded-content{display:none;background-color:white;padding:5px} -.embedded-item .item-content{max-height:25em;overflow:auto} -.embedded-item.visualization .item-content{overflow:hidden} +.embedded-item{margin:0em auto;width:90%;-moz-border-radius:0.5em;-webkit-border-radius:0.5em;border-radius:0.5em}.embedded-item .expanded-content{display:none;background-color:white} +.embedded-item .item-content{max-height:45em;overflow:auto} .embedded-item>.title{vertical-align:top;text-align:center;font-weight:bold;padding-bottom:5px} .embedded-item.placeholder .content{padding:0.5em 0.5em;font-style:italic;text-align:center} -table.annotated-item{width:100%;border-collapse:collapse} -table.annotated-item td,th{padding:0} -table.annotated-item .annotation{padding-left:2em;width:40%} -table.annotated-item td.annotation{vertical-align:text-top;padding-top:1em} +.embedded-item p{background:inherit;margin-top:0;margin-bottom:0} +.embedded-item table.annotated-item{width:100%;border-collapse:collapse} +.embedded-item table.annotated-item td,.embedded-item th{padding:0} +.embedded-item table.annotated-item .annotation{padding-left:2em;width:40%} +.embedded-item table.annotated-item td.annotation{vertical-align:text-top;padding-top:1em} +.embedded-item.display{padding:5px 10px 10px 10px} +.embedded-item.history{background-color:#C1C9E5} +.embedded-item.dataset{background-color:#CFC}.embedded-item.dataset .item-content{padding:5px} +.embedded-item.workflow{background-color:#FBDDB3}.embedded-item.workflow .item-content{padding:5px} +.embedded-item.visualization{background-color:#BBBBBB}.embedded-item.visualization .item-content{overflow:hidden;height:100%}.embedded-item.visualization .item-content iframe{min-height:320px;margin-bottom:-4px} diff -r f26c2543ff053b9ff31617bc03f99d505302ecda -r 31f05a12912be544f59a85239e584eeac15a4b98 static/style/src/less/embed_item.less --- a/static/style/src/less/embed_item.less +++ b/static/style/src/less/embed_item.less @@ -4,6 +4,54 @@ -moz-border-radius: 0.5em; -webkit-border-radius: 0.5em; border-radius: 0.5em; + + .expanded-content { + display: none; + background-color: white; + } + + .item-content { + max-height: 45em; + overflow: auto; + } + + & > .title { + vertical-align: top; + text-align: center; + font-weight: bold; + padding-bottom: 5px; + } + + &.placeholder .content { + padding: 0.5em 0.5em; + font-style: italic; + text-align: center; + } + + p { + background: inherit; + margin-top:0; + margin-bottom:0; + } + + table.annotated-item { + width: 100%; + border-collapse: collapse; + } + + table.annotated-item td,th { + padding: 0; + } + + table.annotated-item .annotation { + padding-left: 2em; + width: 40%; + } + + table.annotated-item td.annotation { + vertical-align: text-top; + padding-top: 1em; + } } .embedded-item.display { @@ -11,89 +59,32 @@ } .embedded-item.history { - background-color:#C1C9E5 -} - -.embedded-item.history p { - background:#C1C9E5 no-repeat 2px 2px; - margin-top:0; - margin-bottom:0; + background-color: #C1C9E5; } .embedded-item.dataset { - background-color:#CFC -} - -.embedded-item.dataset p { - background:#CFC no-repeat 2px 2px; - margin-top:0;margin-bottom:0; + background-color: #CFC; + .item-content { + padding: 5px; + } } .embedded-item.workflow { - background-color:#FBDDB3 -} - -.embedded-item.workflow p { - background:#FBDDB3 no-repeat 2px 2px; - margin-top:0; - margin-bottom:0; + background-color: #FBDDB3; + .item-content { + padding: 5px; + } } .embedded-item.visualization { - background-color:#BBBBBB + background-color: #BBBBBB; + .item-content { + overflow: hidden; + height: 100%; + iframe { + min-height: 320px; + //TODO: hack to fix small gap after iframe + margin-bottom: -4px; + } + } } - -.embedded-item.visualization p { - background:#BBBBBB no-repeat 2px 2px; - margin-top:0; - margin-bottom:0; -} - -.embedded-item.placeholder{} - -.embedded-item .expanded-content { - display: none; - background-color: white; - padding: 5px; -} - -.embedded-item .item-content { - max-height: 25em; - overflow: auto; -} - -.embedded-item.visualization .item-content { - overflow: hidden; -} - -.embedded-item > .title { - vertical-align: top; - text-align: center; - font-weight: bold; - padding-bottom: 5px; -} - -.embedded-item.placeholder .content { - padding: 0.5em 0.5em; - font-style: italic; - text-align: center; -} - -table.annotated-item { - width: 100%; - border-collapse: collapse; -} - -table.annotated-item td,th { - padding: 0; -} - -table.annotated-item .annotation { - padding-left: 2em; - width: 40%; -} - -table.annotated-item td.annotation { - vertical-align: text-top; - padding-top: 1em; -} diff -r f26c2543ff053b9ff31617bc03f99d505302ecda -r 31f05a12912be544f59a85239e584eeac15a4b98 templates/webapps/galaxy/history/embed.mako --- a/templates/webapps/galaxy/history/embed.mako +++ b/templates/webapps/galaxy/history/embed.mako @@ -1,4 +1,3 @@ -##<%inherit file="/embed_base.mako"/><%namespace file="/display_common.mako" import="*" /> ## Some duplication with embed_base here, needed a way to override the main embedded-item html for histories diff -r f26c2543ff053b9ff31617bc03f99d505302ecda -r 31f05a12912be544f59a85239e584eeac15a4b98 templates/webapps/galaxy/page/display.mako --- a/templates/webapps/galaxy/page/display.mako +++ b/templates/webapps/galaxy/page/display.mako @@ -10,7 +10,8 @@ // (b) ... $('.embedded-item').each( function() { var container = $(this); - if( container.hasClass( 'history' ) ){ return; } + if( container.hasClass( 'history' ) + || container.hasClass( 'visualization' ) ){ return; } // Show embedded item. var show_embedded_item = function() { @@ -119,10 +120,6 @@ .embedded-item.history .toggle { display: inline; } - .embedded-item.history .expanded-content { - /* generates a fake wide border */ - padding: 4px; - } /** wraps around the history */ .embedded-item.history .item-content { background-color: white; @@ -138,6 +135,11 @@ .annotated-history-panel .history-controls { margin: 0px 0px 16px 0px; } + + /* ---------------------------- visualizations */ + .embedded-item.visualization .item-content { + max-height: none; + } </style></%def> diff -r f26c2543ff053b9ff31617bc03f99d505302ecda -r 31f05a12912be544f59a85239e584eeac15a4b98 templates/webapps/galaxy/visualization/embed_in_frame.mako --- /dev/null +++ b/templates/webapps/galaxy/visualization/embed_in_frame.mako @@ -0,0 +1,78 @@ +<%namespace file="/display_common.mako" import="*" /> + +<% + import_href = h.url_for( controller='visualization', action='imp', id=encoded_visualization_id ) + display_href = h.url_for( controller='visualization', action='display_by_username_and_slug', + username=item.user.username, slug=item.slug ) +%> +<div id="visualization-${encoded_visualization_id}" class='embedded-item display visualization'> + <div class='title'> + <div style="float: left"> + <a class="expand-content-btn icon-button toggle-expand" href="${display_href}" + title="Show or hide visualization"></a> + </div> + <div style="float: right;"> + <a title="Import" class="icon-button import" href="${import_href}"></a> + <a title="View" class="icon-button go-to-full-screen" href="${display_href}"></a> + </div> + <h4> + <a class="toggle-embed" href="${display_href}" title="Show or hide visualization"> + Galaxy Visualization | ${get_item_name( item )} + </a> + </h4> + %if hasattr( item, "annotation") and item.annotation: + <div class="annotation">${item.annotation}</div> + %endif + </div> + ##<div class='summary-content'> + ## currently, no summary content for visualization + ## could do the title or caption, whatever... + ##</div> + <div class='expanded-content'> + <div class='item-content'> + </div> + </div> +</div> + +<script type="text/javascript"> +// Embedding the same visualization more than once will confuse DOM ids. +// In order to handle this, find this script and cache the previous node (the div above). +// (Since we need thisScript to be locally scoped or it will get overwritten, enclose in self-calling function) +(function(){ + var scripts = document.getElementsByTagName( 'script' ), + // this is executed immediately, so the last script will be this script + thisScript = scripts[ scripts.length - 1 ], + $embeddedObj = $( thisScript ).prev(); + + /** check for an existing iframe for this visualization, adding one to the item-content if needed */ + function addVisualizationIFrame(){ + var $embeddedObj = $( thisScript ).prev(), + $itemContent = $embeddedObj.find( '.expanded-content .item-content' ), + $iframe = $itemContent.find( 'iframe' ); + if( $iframe.size() ){ return $iframe; } + return $itemContent.html([ + '<iframe frameborder="0" width="100%" height="100%" ', + 'sandbox="allow-forms allow-same-origin allow-scripts" ', + 'src="/visualization/saved?id=${encoded_visualization_id}&embedded=True">', + '</iframe>' + ].join('')).find( 'iframe' ); + } + + /** 4 elements change when expanding - toggle them all, add the iframe and prevent the url change */ + function toggleExpanded( ev ){ + var $embeddedObj = $( thisScript ).prev(); + $embeddedObj.find( '.expand-content-btn' ).toggleClass( 'toggle-expand' ).toggleClass( 'toggle' ); + $embeddedObj.find( ".summary-content" ).slideToggle( "fast" ); + $embeddedObj.find( ".annotation" ).slideToggle( "fast" ); + $embeddedObj.find( ".expanded-content" ).slideToggle( "fast" ); + addVisualizationIFrame(); + ev.preventDefault(); + } + + // add expansion to +/- btn and title + $(function(){ + $embeddedObj.find( '.expand-content-btn' ).click( toggleExpanded ); + $embeddedObj.find( '.toggle-embed' ).click( toggleExpanded ); + }); +})(); +</script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Trigger change event manually
by commits-noreply＠bitbucket.org 12 Nov '14

12 Nov '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f26c2543ff05/ Changeset: f26c2543ff05 User: guerler Date: 2014-11-12 16:30:59+00:00 Summary: ToolForm: Trigger change event manually Affected #: 3 files diff -r d7450b2567fb56f93ccc0191a7059ebb46b23cc5 -r f26c2543ff053b9ff31617bc03f99d505302ecda 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 @@ -239,6 +239,7 @@ } } field.update(new_options); + field.trigger('change'); console.debug('Updating options for ' + input_id); } } diff -r d7450b2567fb56f93ccc0191a7059ebb46b23cc5 -r f26c2543ff053b9ff31617bc03f99d505302ecda static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -239,6 +239,7 @@ } } field.update(new_options); + field.trigger('change'); console.debug('Updating options for ' + input_id); } } diff -r d7450b2567fb56f93ccc0191a7059ebb46b23cc5 -r f26c2543ff053b9ff31617bc03f99d505302ecda 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(["utils/utils","utils/deferred","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-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","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-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(!this.is_dynamic){return}var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(JSON.stringify(p.options)!=JSON.stringify(u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var r=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:r},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({collection:n});q.render();n.fetch();this.$el.append(q.$el)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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