From 5f1b7d5a5060c3c45601b499a953113e0b1b3125 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 3 Aug 2017 15:01:57 +0200 Subject: [PATCH 01/14] Show verison button in workflow editor and trigger on_change --- client/galaxy/scripts/mvc/tool/tool-form-base.js | 3 ++- client/galaxy/scripts/mvc/workflow/workflow-forms.js | 2 +- client/galaxy/scripts/mvc/workflow/workflow-manager.js | 1 + client/galaxy/scripts/mvc/workflow/workflow-node.js | 1 + 4 files changed, 5 insertions(+), 2 deletions(-) diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js index c26c35e96f7e..6c804b21d59b 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-base.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js @@ -156,7 +156,8 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view // queue model request self.deferred.reset(); self.deferred.execute( function( process ) { - self._buildModel( process, { id : id, version : version } ) + self._buildModel( process, { id : id, version : version } ); + self.model.get( 'postchange' )( process, self ); }); } }); diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js index 59327f581496..0e533872310b 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js @@ -37,7 +37,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func text_disable : 'Set at Runtime', narrow : true, initial_errors : true, - sustain_version : true, + sustain_version : false, cls : 'ui-portlet-narrow', postchange : function( process, form ) { var options = form.model.attributes; diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js index 4e03d37b1319..1c06b827bf5e 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js @@ -182,6 +182,7 @@ function( Connector, Toastr ) { id : node.id, type : node.type, content_id : node.content_id, + tool_version:node.tool_version, tool_state : node.tool_state, errors : node.errors, input_connections : input_connections, diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index ed0ac71e1e6a..2e41301e1935 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -185,6 +185,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { var nodeView = node.nodeView; this.tool_state = data.tool_state; this.config_form = data.config_form; + this.tool_version = this.config_form.version; this.errors = data.errors; this.annotation = data['annotation']; this.label = data.label; From 25e05b62c7b529b0379e3ff50fc75ccb5b8c28b6 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 3 Aug 2017 17:49:12 +0200 Subject: [PATCH 02/14] Do postchange action only when modifiying tool versions in the workflow editor --- client/galaxy/scripts/mvc/tool/tool-form-base.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js index 6c804b21d59b..29ecfb3f9fe6 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-base.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js @@ -157,7 +157,10 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view self.deferred.reset(); self.deferred.execute( function( process ) { self._buildModel( process, { id : id, version : version } ); - self.model.get( 'postchange' )( process, self ); + if ( options.hasOwnProperty( "workflow" ) ) { + // this is needed for notifying the workflow editor form + self.model.get( 'postchange' )( process, self ); + }; }); } }); From 5afe490822325d4aa6c9be726183175743dc88f6 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 3 Aug 2017 17:49:50 +0200 Subject: [PATCH 03/14] Fix qunit test --- client/galaxy/scripts/mvc/workflow/workflow-node.js | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index 2e41301e1935..af4b08c84d26 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -185,7 +185,12 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { var nodeView = node.nodeView; this.tool_state = data.tool_state; this.config_form = data.config_form; - this.tool_version = this.config_form.version; + if (this.config_form) { + this.tool_version = this.config_form.version; + } else { + // empty config_form should only happen in qunit tests + this.tool_version = null; + } this.errors = data.errors; this.annotation = data['annotation']; this.label = data.label; @@ -238,4 +243,4 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { } }); return Node; -}); \ No newline at end of file +}); From 36ce9113f7ccb6372bc2d1f8e92e95a8aafdd066 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 3 Aug 2017 17:53:10 +0200 Subject: [PATCH 04/14] Keep spacing consistent (thx @nsoranzo) --- .../galaxy/scripts/mvc/workflow/workflow-manager.js | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js index 1c06b827bf5e..10c6273fe1dc 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js @@ -182,16 +182,16 @@ function( Connector, Toastr ) { id : node.id, type : node.type, content_id : node.content_id, - tool_version:node.tool_version, + tool_version : node.tool_version, tool_state : node.tool_state, errors : node.errors, input_connections : input_connections, position : $(node.element).position(), - annotation: node.annotation, - post_job_actions: node.post_job_actions, - uuid: node.uuid, - label: node.label, - workflow_outputs: node.workflow_outputs + annotation : node.annotation, + post_job_actions : node.post_job_actions, + uuid : node.uuid, + label : node.label, + workflow_outputs : node.workflow_outputs }; nodes[ node.id ] = node_data; }); From 526e98e372e61747b1e3cd4b86a04603ca08959b Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sat, 5 Aug 2017 18:14:47 +0200 Subject: [PATCH 05/14] Reset outputs when changing tool versions in wf-editor --- client/galaxy/scripts/mvc/tool/tool-form-base.js | 5 ++++- client/galaxy/scripts/mvc/workflow/workflow-forms.js | 10 +++++++++- client/galaxy/scripts/mvc/workflow/workflow-node.js | 1 + 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js index 29ecfb3f9fe6..f68ea2be302a 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-base.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js @@ -156,10 +156,13 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view // queue model request self.deferred.reset(); self.deferred.execute( function( process ) { - self._buildModel( process, { id : id, version : version } ); if ( options.hasOwnProperty( "workflow" ) ) { // this is needed for notifying the workflow editor form + options.old_version = options.version; + options.version = version; self.model.get( 'postchange' )( process, self ); + } else { + self._buildModel( process, { id : id, version : version } ); }; }); } diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js index 0e533872310b..b49be8c9caa3 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js @@ -59,7 +59,15 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func // module information for the tool to update the workflow // state stored on the client with. User needs to save // for this to take effect. - self.node.update_field_data( data ); + + // update_field_data can't deal with output changes, + // as can happen when the tool version changes so we re-initialize this node. + if (options.hasOwnProperty( "old_version" ) && options.old_version !== options.version) { + self.node.init_field_data( data ); + } else { + self.node.update_field_data( data ); + } + Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Received new model.', data ); process.resolve(); }, diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index af4b08c84d26..8eda5c611bfb 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -158,6 +158,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { this.errors = data.errors; this.tooltip = data.tooltip ? data.tooltip : ""; this.annotation = data.annotation; + this.output_terminals = {}; // removes outputs when switching tool versions this.post_job_actions = data.post_job_actions ? data.post_job_actions : {}; this.label = data.label; this.uuid = data.uuid; From db2ea853f699bf6b55b67cf7199ab355196910bc Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 6 Aug 2017 15:43:59 +0200 Subject: [PATCH 06/14] Now thing are mostly working -- input and output connections are correctly altered ... but saving the workflow and reloading occasionally loads the wrong workflow --- .../scripts/mvc/workflow/workflow-forms.js | 8 +---- .../scripts/mvc/workflow/workflow-node.js | 30 +++++++++++++++++++ .../scripts/mvc/workflow/workflow-view.js | 1 + 3 files changed, 32 insertions(+), 7 deletions(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js index b49be8c9caa3..db407dec97b3 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js @@ -60,13 +60,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func // state stored on the client with. User needs to save // for this to take effect. - // update_field_data can't deal with output changes, - // as can happen when the tool version changes so we re-initialize this node. - if (options.hasOwnProperty( "old_version" ) && options.old_version !== options.version) { - self.node.init_field_data( data ); - } else { - self.node.update_field_data( data ); - } + self.node.update_field_data( data ); Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Received new model.', data ); process.resolve(); diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index 8eda5c611bfb..e1e385a15286 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -184,6 +184,31 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { update_field_data : function( data ) { var node = this; var nodeView = node.nodeView; + // remove unused output views and remove pre-exisiting output views from data.data_outputs, + // so that these are not added twice. + _.each(nodeView.outputViews, function(output_view) { + var cur_name = output_view.output.name; + var data_names = data.data_outputs; + var delete_terminal = true; + $.each(data_names, function(i, data_output) { + console.log(data_output); + if (data_output.name === cur_name) { + delete_terminal = false; + data.data_outputs.splice(i, 1); + } + }); + if (delete_terminal) { + _.each(output_view.terminalElement.terminal.connectors, function (x) { + if (x) { + x.destroy(); + } + }) + output_view.remove(); + } + }); + + this.output_terminals = {}, + nodeView.outputViews = {}; this.tool_state = data.tool_state; this.config_form = data.config_form; if (this.config_form) { @@ -213,6 +238,9 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { _.each( _.difference( _.values( nodeView.terminalViews ), _.values( newTerminalViews ) ), function( unusedView ) { unusedView.el.terminal.destroy(); } ); + $.each( data.data_outputs, function( i, output ) { + nodeView.addDataOutput( output ); + } ); nodeView.terminalViews = newTerminalViews; node.nodeView.render(); // In general workflow editor assumes tool outputs don't change in # or @@ -230,6 +258,8 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { // If active, reactivate with new config_form this.markChanged(); this.redraw(); + // nodeView.render(); + this.app.workflow.node_changed( this, true); }, error : function ( text ) { var b = $(this.element).find( ".toolFormBody" ); diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js index 3de3bb032421..8d7b965e0673 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-view.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js @@ -658,6 +658,7 @@ define([ var cls = 'right-content'; var id = cls + '-' + node.id; var $container = $( '#' + cls ); + $container.find( '#' + id ).remove(); if ( content && $container.find( '#' + id ).length == 0 ) { var $el = $( '
' ); var form_wrapper = null; From ea1f4f866658e77465d1272b4d7f37bb85ee488b Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 6 Aug 2017 16:38:51 +0200 Subject: [PATCH 07/14] Fix the occasional loading of the wrong workflow. Turns out that sometimes the tool_version is undefined (i.e) if the exact node had not been manipulated, but config_form.version is always up to date --- client/galaxy/scripts/mvc/workflow/workflow-manager.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js index 10c6273fe1dc..8a30e3f57da8 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js @@ -182,7 +182,7 @@ function( Connector, Toastr ) { id : node.id, type : node.type, content_id : node.content_id, - tool_version : node.tool_version, + tool_version : node.config_form.version, tool_state : node.tool_state, errors : node.errors, input_connections : input_connections, From bc95f5e81b46a0bee54f6ffdd5c3a6615258af20 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 7 Aug 2017 11:08:11 +0200 Subject: [PATCH 08/14] Now adding/removing datasets and multiple version switches work fine, but PJA parameters are still problematic --- .../scripts/mvc/workflow/workflow-node.js | 57 ++++++++++--------- 1 file changed, 30 insertions(+), 27 deletions(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index e1e385a15286..63e220ead1ab 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -158,7 +158,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { this.errors = data.errors; this.tooltip = data.tooltip ? data.tooltip : ""; this.annotation = data.annotation; - this.output_terminals = {}; // removes outputs when switching tool versions + // this.output_terminals = {}; // removes outputs when switching tool versions this.post_job_actions = data.post_job_actions ? data.post_job_actions : {}; this.label = data.label; this.uuid = data.uuid; @@ -186,37 +186,43 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { var nodeView = node.nodeView; // remove unused output views and remove pre-exisiting output views from data.data_outputs, // so that these are not added twice. - _.each(nodeView.outputViews, function(output_view) { + var unused_outputs = []; + // nodeView.outputViews contains pre-existing outputs, + // while data.data_output contains what should be displayed. + // Now we gather the unused outputs + console.log(nodeView.outputViews); + $.each(nodeView.outputViews, function(i, output_view) { var cur_name = output_view.output.name; var data_names = data.data_outputs; - var delete_terminal = true; - $.each(data_names, function(i, data_output) { - console.log(data_output); - if (data_output.name === cur_name) { - delete_terminal = false; - data.data_outputs.splice(i, 1); + var cur_name_in_data_outputs = false; + _.each(data_names, function(data_name) { + if (data_name.name == cur_name) { + cur_name_in_data_outputs = true; } }); - if (delete_terminal) { - _.each(output_view.terminalElement.terminal.connectors, function (x) { - if (x) { - x.destroy(); - } - }) - output_view.remove(); + if (cur_name_in_data_outputs === false) { + unused_outputs.push(cur_name) } }); - this.output_terminals = {}, - nodeView.outputViews = {}; + // Remove the unused outputs + _.each(unused_outputs, function(unused_output) { + _.each(nodeView.outputViews[unused_output].terminalElement.terminal.connectors, function(x) { + if (x) { + x.destroy(); // Removes the noodle connectors + } + }); + nodeView.outputViews[unused_output].remove(); // removes the rendered output + delete nodeView.outputViews[unused_output]; // removes the reference to the output + delete node.output_terminals[unused_output]; // removes the output terminal + }); + $.each( data.data_outputs, function( i, output ) { + if (!nodeView.outputViews[output.name]) { + nodeView.addDataOutput(output); // add data output if it does not yet exist + } + }); this.tool_state = data.tool_state; this.config_form = data.config_form; - if (this.config_form) { - this.tool_version = this.config_form.version; - } else { - // empty config_form should only happen in qunit tests - this.tool_version = null; - } this.errors = data.errors; this.annotation = data['annotation']; this.label = data.label; @@ -238,9 +244,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { _.each( _.difference( _.values( nodeView.terminalViews ), _.values( newTerminalViews ) ), function( unusedView ) { unusedView.el.terminal.destroy(); } ); - $.each( data.data_outputs, function( i, output ) { - nodeView.addDataOutput( output ); - } ); + nodeView.terminalViews = newTerminalViews; node.nodeView.render(); // In general workflow editor assumes tool outputs don't change in # or @@ -258,7 +262,6 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { // If active, reactivate with new config_form this.markChanged(); this.redraw(); - // nodeView.render(); this.app.workflow.node_changed( this, true); }, error : function ( text ) { From 92fedc0ae86127d670f3ff8e829d07ee657f30d7 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 7 Aug 2017 14:06:10 +0200 Subject: [PATCH 09/14] Fix logic for adding and removing outputs --- client/galaxy/scripts/mvc/workflow/workflow-forms.js | 1 - client/galaxy/scripts/mvc/workflow/workflow-manager.js | 2 +- client/galaxy/scripts/mvc/workflow/workflow-node.js | 9 +++++---- client/galaxy/scripts/mvc/workflow/workflow-view.js | 7 +++++-- 4 files changed, 11 insertions(+), 8 deletions(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js index db407dec97b3..24fe716d60a3 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js @@ -37,7 +37,6 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func text_disable : 'Set at Runtime', narrow : true, initial_errors : true, - sustain_version : false, cls : 'ui-portlet-narrow', postchange : function( process, form ) { var options = form.model.attributes; diff --git a/client/galaxy/scripts/mvc/workflow/workflow-manager.js b/client/galaxy/scripts/mvc/workflow/workflow-manager.js index 8a30e3f57da8..299c792a2006 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-manager.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-manager.js @@ -309,7 +309,7 @@ function( Connector, Toastr ) { if ( this.active_node == node && force ) { // Force changes to be saved even on new connection (previously dumped) this.check_changes_in_active_form(); - this.app.showForm( node.config_form, node ); + this.app.showForm( node.config_form, node, force ); } this.app.showWorkflowParameters(); }, diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index 63e220ead1ab..4374d854169d 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -154,6 +154,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { } this.name = data.name; this.config_form = data.config_form; + this.tool_version = this.config_form && this.config_form.version; this.tool_state = data.tool_state; this.errors = data.errors; this.tooltip = data.tooltip ? data.tooltip : ""; @@ -184,13 +185,12 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { update_field_data : function( data ) { var node = this; var nodeView = node.nodeView; - // remove unused output views and remove pre-exisiting output views from data.data_outputs, + // remove unused output views and remove pre-existing output views from data.data_outputs, // so that these are not added twice. var unused_outputs = []; // nodeView.outputViews contains pre-existing outputs, // while data.data_output contains what should be displayed. // Now we gather the unused outputs - console.log(nodeView.outputViews); $.each(nodeView.outputViews, function(i, output_view) { var cur_name = output_view.output.name; var data_names = data.data_outputs; @@ -223,6 +223,8 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { }); this.tool_state = data.tool_state; this.config_form = data.config_form; + this.force_refesh = this.config_form && this.tool_version !== this.config_form.version; + this.tool_version = this.config_form && this.config_form.version; this.errors = data.errors; this.annotation = data['annotation']; this.label = data.label; @@ -262,7 +264,6 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { // If active, reactivate with new config_form this.markChanged(); this.redraw(); - this.app.workflow.node_changed( this, true); }, error : function ( text ) { var b = $(this.element).find( ".toolFormBody" ); @@ -273,7 +274,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { this.app.workflow.node_changed( this ); }, markChanged: function() { - this.app.workflow.node_changed( this ); + this.app.workflow.node_changed( this, this.force_refesh ); } }); return Node; diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js index 8d7b965e0673..568fd357d2f2 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-view.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js @@ -653,12 +653,15 @@ define([ $( '#edit-attributes' ).show(); }, - showForm: function ( content, node ) { + showForm: function ( content, node, force ) { var self = this; var cls = 'right-content'; var id = cls + '-' + node.id; var $container = $( '#' + cls ); - $container.find( '#' + id ).remove(); + if (force) { + $container.find( '#' + id ).remove(); + $( '
').remove(); + } if ( content && $container.find( '#' + id ).length == 0 ) { var $el = $( '
' ); var form_wrapper = null; From 1c286b158a8304380f499709b2f14c958b6fe203 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 7 Aug 2017 14:13:12 +0200 Subject: [PATCH 10/14] Remove extra newlines --- client/galaxy/scripts/mvc/workflow/workflow-forms.js | 2 -- client/galaxy/scripts/mvc/workflow/workflow-node.js | 1 - 2 files changed, 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js index 24fe716d60a3..0eb059caa73c 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js @@ -58,9 +58,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func // module information for the tool to update the workflow // state stored on the client with. User needs to save // for this to take effect. - self.node.update_field_data( data ); - Galaxy.emit.debug( 'tool-form-workflow::postchange()', 'Received new model.', data ); process.resolve(); }, diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index 4374d854169d..857866720a6c 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -246,7 +246,6 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { _.each( _.difference( _.values( nodeView.terminalViews ), _.values( newTerminalViews ) ), function( unusedView ) { unusedView.el.terminal.destroy(); } ); - nodeView.terminalViews = newTerminalViews; node.nodeView.render(); // In general workflow editor assumes tool outputs don't change in # or From 2e95026317e2e781163cf8bd4449bfd5ddfb894f Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 7 Aug 2017 14:15:50 +0200 Subject: [PATCH 11/14] Remove unused old_version variable --- client/galaxy/scripts/mvc/tool/tool-form-base.js | 1 - 1 file changed, 1 deletion(-) diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js index f68ea2be302a..736096dd53ae 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-base.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js @@ -158,7 +158,6 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view self.deferred.execute( function( process ) { if ( options.hasOwnProperty( "workflow" ) ) { // this is needed for notifying the workflow editor form - options.old_version = options.version; options.version = version; self.model.get( 'postchange' )( process, self ); } else { From 31c423a45a4186c41981f71d41a590177bad033d Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 7 Aug 2017 16:16:39 +0200 Subject: [PATCH 12/14] Fix typo and remove leftover comment (thanks @nsoranzo) --- client/galaxy/scripts/mvc/workflow/workflow-node.js | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index 857866720a6c..722fc59e979c 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -159,7 +159,6 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { this.errors = data.errors; this.tooltip = data.tooltip ? data.tooltip : ""; this.annotation = data.annotation; - // this.output_terminals = {}; // removes outputs when switching tool versions this.post_job_actions = data.post_job_actions ? data.post_job_actions : {}; this.label = data.label; this.uuid = data.uuid; @@ -223,7 +222,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { }); this.tool_state = data.tool_state; this.config_form = data.config_form; - this.force_refesh = this.config_form && this.tool_version !== this.config_form.version; + this.force_refresh = this.config_form && this.tool_version !== this.config_form.version; this.tool_version = this.config_form && this.config_form.version; this.errors = data.errors; this.annotation = data['annotation']; @@ -273,7 +272,7 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { this.app.workflow.node_changed( this ); }, markChanged: function() { - this.app.workflow.node_changed( this, this.force_refesh ); + this.app.workflow.node_changed( this, this.force_refresh ); } }); return Node; From df91881c1f4dba06a9fb6a1720db68d059664041 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 8 Aug 2017 17:20:57 +0200 Subject: [PATCH 13/14] Remove unused workflow outputs --- client/galaxy/scripts/mvc/workflow/workflow-node.js | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index 722fc59e979c..18c68071bbb9 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -215,6 +215,11 @@ define(['mvc/workflow/workflow-view-node'], function( NodeView ) { delete nodeView.outputViews[unused_output]; // removes the reference to the output delete node.output_terminals[unused_output]; // removes the output terminal }); + $.each( node.workflow_outputs, function(i, wf_output){ + if (wf_output && !node.output_terminals[wf_output.output_name]) { + node.workflow_outputs.splice(i, 1); // removes output from list of workflow outputs + } + }); $.each( data.data_outputs, function( i, output ) { if (!nodeView.outputViews[output.name]) { nodeView.addDataOutput(output); // add data output if it does not yet exist From 73f4141d96ad54c25fdf7a3ffb458f2b1933e14e Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 14 Aug 2017 00:21:25 +0200 Subject: [PATCH 14/14] Add static JS --- static/maps/mvc/tool/tool-form-base.js.map | 2 +- static/maps/mvc/workflow/workflow-forms.js.map | 2 +- static/maps/mvc/workflow/workflow-manager.js.map | 2 +- static/maps/mvc/workflow/workflow-node.js.map | 2 +- static/maps/mvc/workflow/workflow-view.js.map | 2 +- static/scripts/bundled/admin.bundled.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 11 ++++++----- static/scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 2 +- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/bundled/login.bundled.js.map | 2 +- static/scripts/mvc/tool/tool-form-base.js | 2 +- static/scripts/mvc/workflow/workflow-forms.js | 2 +- static/scripts/mvc/workflow/workflow-manager.js | 2 +- static/scripts/mvc/workflow/workflow-node.js | 2 +- static/scripts/mvc/workflow/workflow-view.js | 2 +- 16 files changed, 21 insertions(+), 20 deletions(-) diff --git a/static/maps/mvc/tool/tool-form-base.js.map b/static/maps/mvc/tool/tool-form-base.js.map index 3f495c062c28..e63f50aa85d7 100644 --- a/static/maps/mvc/tool/tool-form-base.js.map +++ b/static/maps/mvc/tool/tool-form-base.js.map @@ -1 +1 @@ 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0 */\n/***/ function(module, exports, __webpack_require__) {\n\n\t/* WEBPACK VAR INJECTION */(function(_) {var jQuery = __webpack_require__(1),\n\t $ = jQuery,\n\t GalaxyApp = __webpack_require__(49).GalaxyApp,\n\t AdminPanel = __webpack_require__(100),\n\t FormWrapper = __webpack_require__(59),\n\t GridView = __webpack_require__(12),\n\t Ui = __webpack_require__(5),\n\t QueryStringParsing = __webpack_require__(26),\n\t Router = __webpack_require__(52),\n\t Page = __webpack_require__(50);\n\t\n\twindow.app = function app(options, bootstrapped) {\n\t window.Galaxy = new GalaxyApp(options, bootstrapped);\n\t Galaxy.debug('admin app');\n\t\n\t /** Routes */\n\t var AdminRouter = Router.extend({\n\t routes: {\n\t '(/)admin(/)users': 'show_users',\n\t '(/)admin(/)roles': 'show_roles',\n\t '(/)admin(/)forms(/)(:form_id)': 'show_forms'\n\t },\n\t\n\t authenticate: function (args, name) {\n\t return Galaxy.user && Galaxy.user.id && Galaxy.user.get('is_admin');\n\t },\n\t\n\t show_users: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/users_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_roles: function () {\n\t this.page.display(new GridView({ url_base: Galaxy.root + 'admin/roles_list', url_data: Galaxy.params, dict_format: true }));\n\t },\n\t\n\t show_forms: function (form_id) {\n\t var form_defs = {\n\t reset_user_password: {\n\t title: 'Reset passwords',\n\t url: 'admin/reset_user_password?id=' + QueryStringParsing.get('id'),\n\t icon: 'fa-user',\n\t submit_title: 'Save new password',\n\t redirect: 'admin/users'\n\t },\n\t manage_roles_and_groups_for_user: {\n\t url: 'admin/manage_roles_and_groups_for_user?id=' + QueryStringParsing.get('id'),\n\t icon: 'fa-users',\n\t redirect: 'admin/users'\n\t },\n\t manage_users_and_groups_for_role: {\n\t url: 'admin/manage_users_and_groups_for_role?id=' + QueryStringParsing.get('id'),\n\t redirect: 'admin/roles'\n\t },\n\t rename_role: {\n\t url: 'admin/rename_role?id=' + QueryStringParsing.get('id'),\n\t redirect: 'admin/roles'\n\t },\n\t create_role: {\n\t url: 'admin/create_role?id=' + QueryStringParsing.get('id'),\n\t redirect: 'admin/roles'\n\t }\n\t };\n\t this.page.display(new FormWrapper.View(form_defs[form_id]));\n\t }\n\t });\n\t\n\t $(function () {\n\t _.extend(options.config, { active_view: 'admin' });\n\t Galaxy.page = new Page.View(_.extend(options, {\n\t Left: AdminPanel,\n\t Router: AdminRouter\n\t }));\n\t });\n\t};\n\t/* WEBPACK VAR INJECTION */}.call(exports, __webpack_require__(3)))\n\n/***/ },\n/* 1 */,\n/* 2 */,\n/* 3 */,\n/* 4 */,\n/* 5 */\n/***/ function(module, exports, __webpack_require__) {\n\n\tvar __WEBPACK_AMD_DEFINE_ARRAY__, __WEBPACK_AMD_DEFINE_RESULT__;/* WEBPACK VAR INJECTION */(function(Backbone, $, _) {/**\n\t * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc.\n\t */\n\t!(__WEBPACK_AMD_DEFINE_ARRAY__ = [__webpack_require__(4), __webpack_require__(15), __webpack_require__(40), __webpack_require__(14), __webpack_require__(36), __webpack_require__(11), __webpack_require__(8)], __WEBPACK_AMD_DEFINE_RESULT__ = function (Utils, Select, Slider, Options, Drilldown, Buttons, Modal) {\n\t\n\t /** Label wrapper */\n\t var Label = Backbone.View.extend({\n\t tagName: 'label',\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.tagName = options.tagName || this.tagName;\n\t this.setElement($('<' + this.tagName + '/>'));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t title: function (new_title) {\n\t this.model.set('title', new_title);\n\t },\n\t value: function () {\n\t return this.model.get('title');\n\t },\n\t render: function () {\n\t this.$el.removeClass().addClass('ui-label').addClass(this.model.get('cls')).html(this.model.get('title'));\n\t return this;\n\t }\n\t });\n\t\n\t /** Displays messages used e.g. in the tool form */\n\t var Message = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t message: null,\n\t status: 'info',\n\t cls: '',\n\t persistent: false,\n\t fade: true\n\t }).set(options);\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t update: function (options) {\n\t this.model.set(options);\n\t },\n\t render: function () {\n\t this.$el.removeClass().addClass('ui-message').addClass(this.model.get('cls'));\n\t var status = this.model.get('status');\n\t if (this.model.get('large')) {\n\t this.$el.addClass((status == 'success' && 'done' || status == 'danger' && 'error' || status) + 'messagelarge');\n\t } else {\n\t this.$el.addClass('alert').addClass('alert-' + status);\n\t }\n\t if (this.model.get('message')) {\n\t this.$el.html(this.messageForDisplay());\n\t this.$el[this.model.get('fade') ? 'fadeIn' : 'show']();\n\t this.timeout && window.clearTimeout(this.timeout);\n\t if (!this.model.get('persistent')) {\n\t var self = this;\n\t this.timeout = window.setTimeout(function () {\n\t self.model.set('message', '');\n\t }, 3000);\n\t }\n\t } else {\n\t this.$el.fadeOut();\n\t }\n\t return this;\n\t },\n\t messageForDisplay: function () {\n\t return _.escape(this.model.get('message'));\n\t }\n\t });\n\t\n\t var UnescapedMessage = Message.extend({\n\t messageForDisplay: function () {\n\t return this.model.get('message');\n\t }\n\t });\n\t\n\t /** Renders an input element used e.g. in the tool form */\n\t var Input = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model({\n\t type: 'text',\n\t placeholder: '',\n\t disabled: false,\n\t readonly: false,\n\t visible: true,\n\t cls: '',\n\t area: false,\n\t color: null,\n\t style: null\n\t }).set(options);\n\t this.tagName = this.model.get('area') ? 'textarea' : 'input';\n\t this.setElement($('<' + this.tagName + '/>'));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t events: {\n\t 'input': '_onchange'\n\t },\n\t value: function (new_val) {\n\t new_val !== undefined && this.model.set('value', typeof new_val === 'string' ? new_val : '');\n\t return this.model.get('value');\n\t },\n\t render: function () {\n\t var self = this;\n\t this.$el.removeClass().addClass('ui-' + this.tagName).addClass(this.model.get('cls')).addClass(this.model.get('style')).attr('id', this.model.id).attr('type', this.model.get('type')).attr('placeholder', this.model.get('placeholder')).css('color', this.model.get('color') || '').css('border-color', this.model.get('color') || '');\n\t var datalist = this.model.get('datalist');\n\t if ($.isArray(datalist) && datalist.length > 0) {\n\t this.$el.autocomplete({ source: function (request, response) {\n\t response(self.model.get('datalist'));\n\t },\n\t change: function () {\n\t self._onchange();\n\t } });\n\t }\n\t if (this.model.get('value') !== this.$el.val()) {\n\t this.$el.val(this.model.get('value'));\n\t }\n\t _.each(['readonly', 'disabled'], function (attr_name) {\n\t self.model.get(attr_name) ? self.$el.attr(attr_name, true) : self.$el.removeAttr(attr_name);\n\t });\n\t this.$el[this.model.get('visible') ? 'show' : 'hide']();\n\t return this;\n\t },\n\t _onchange: function () {\n\t this.value(this.$el.val());\n\t this.model.get('onchange') && this.model.get('onchange')(this.model.get('value'));\n\t }\n\t });\n\t\n\t /** Creates a hidden element input field used e.g. in the tool form */\n\t var Hidden = Backbone.View.extend({\n\t initialize: function (options) {\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.setElement($('
').append(this.$info = $('
')).append(this.$hidden = $('
')));\n\t this.listenTo(this.model, 'change', this.render, this);\n\t this.render();\n\t },\n\t value: function (new_val) {\n\t new_val !== undefined && this.model.set('value', new_val);\n\t return this.model.get('value');\n\t },\n\t render: function () {\n\t this.$el.attr('id', this.model.id);\n\t this.$hidden.val(this.model.get('value'));\n\t this.model.get('info') ? this.$info.show().text(this.model.get('info')) : this.$info.hide();\n\t return this;\n\t }\n\t });\n\t\n\t /** Creates a upload element input field */\n\t var Upload = Backbone.View.extend({\n\t initialize: function (options) {\n\t var self = this;\n\t this.model = options && options.model || new Backbone.Model(options);\n\t this.setElement($('
').append(this.$info = $('
')).append(this.$file = $('').attr('type', 'file').addClass('ui-margin-bottom')).append(this.$text = $('',"
","
"].join("")}});return{CitationView:n,CitationListView:s}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(a,o,r){n=[i(64),i(58),i(7),i(6)],s=function(e,t,i,n){"use strict";var s=e.FoldoutListItemView,l=e.ListItemView,d=s.extend({className:s.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(e){this.linkTarget=e.linkTarget||"_blank",this.hasUser=e.hasUser,s.prototype.initialize.call(this,e)},_setUpListeners:function(){s.prototype._setUpListeners.call(this),this.listenTo(this.model,"change",function(e,t){a.has(e.changed,"deleted")?this.render():a.has(e.changed,"element_count")&&this.$("> .title-bar .subtitle").replaceWith(this._renderSubtitle())})},_renderSubtitle:function(){return o(this.templates.subtitle(this.model.toJSON(),this))},_getFoldoutPanelOptions:function(){var e=s.prototype._getFoldoutPanelOptions.call(this);return a.extend(e,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var e=this.model?this.model+"":"(no model)";return"DCListItemView("+e+")"}});d.prototype.templates=function(){var e=a.extend({},s.prototype.templates.warnings,{error:i.wrapTemplate(["<% if( model.error ){ %>",'
',n("There was an error getting the data for this collection"),": <%- model.error %>","
","<% } %>"]),purged:i.wrapTemplate(["<% if( model.purged ){ %>",'
',n("This collection has been deleted and removed from disk"),"
","<% } %>"]),deleted:i.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',n("This collection has been deleted"),"
","<% } %>"])}),t=i.wrapTemplate(['
','
','<%- collection.element_identifier || collection.name %>',"
",'
',"
"],"collection"),o=i.wrapTemplate(['
','<% var countText = collection.element_count? ( collection.element_count + " " ) : ""; %>','<% if( collection.collection_type === "list" ){ %>',n("a list of <%- countText %>datasets"),'<% } else if( collection.collection_type === "paired" ){ %>',n("a pair of datasets"),'<% } else if( collection.collection_type === "list:paired" ){ %>',n("a list of <%- countText %>dataset pairs"),'<% } else if( collection.collection_type === "list:list" ){ %>',n("a list of <%- countText %>dataset lists"),"<% } %>","
"],"collection");return a.extend({},s.prototype.templates,{warnings:e,titleBar:t,subtitle:o})}();var c=l.extend({className:l.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DCEListItemView.initialize:",e),l.prototype.initialize.call(this,e)},toString:function(){var e=this.model?this.model+"":"(no model)";return"DCEListItemView("+e+")"}});c.prototype.templates=function(){var e=i.wrapTemplate(['
','
','<%- element.element_identifier %>',"
",'
',"
"],"element");return a.extend({},l.prototype.templates,{titleBar:e})}();var h=t.DatasetListItemView.extend({className:t.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),t.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):r.when()},toString:function(){var e=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+e+")"}});h.prototype.templates=function(){var e=i.wrapTemplate(['
','','
','<%- element.element_identifier %>',"
","
"],"element");return a.extend({},t.DatasetListItemView.prototype.templates,{titleBar:e})}();var u=d.extend({className:d.prototype.className+" dataset-collection-element",_swapNewRender:function(e){d.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+e+")"}});return{DCListItemView:d,DCEListItemView:c,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(1))},function(e,t,i){var n,s;(function(a,o,r){n=[i(83),i(7),i(6)],s=function(e,t,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(e){return a.extend(e,e.object,{element_id:e.id}),delete e.object,e},constructor:function(e,t){e=this._mergeObject(e),this.idAttribute="element_id",o.Model.apply(this,arguments)},parse:function(e,t){var i=e;return i=this._mergeObject(i)}},s=o.Model.extend(t.LoggableMixin).extend(n).extend({_logNamespace:"collections"}),l=o.Collection.extend(t.LoggableMixin).extend({_logNamespace:"collections",model:s,toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),d=e.DatasetAssociation.extend(t.mixin(n,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:a.extend({},e.DatasetAssociation.prototype.defaults,n.defaults),_downloadQueryParameters:function(){return"?to_ext="+this.get("file_ext")+"&hdca_id="+this.get("parent_hdca_id")+"&element_identifier="+this.get("element_identifier")},constructor:function(e,t){this.debug("\t DatasetDCE.constructor:",e,t),n.constructor.call(this,e,t)},hasDetails:function(){return this.elements&&this.elements.length},toString:function(){var e=this.get("element_identifier");return["DatasetDCE(",e,")"].join("")}})),c=l.extend({model:d,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=o.Model.extend(t.LoggableMixin).extend(t.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:l,initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var e=this.get("elements")||[];this.unset("elements",{silent:!0});var t=this;return a.each(e,function(e,i){a.extend(e,{parent_hdca_id:t.get("id")})}),this.elements=new this.collectionClass(e),this.elements},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var e=this.get("populated");return this.isDeletedOrPurged()||e},hasDetails:function(){return 0!==this.elements.length},getVisibleContents:function(e){return this.elements},parse:function(e,t){var i=o.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},delete:function(e){return this.get("deleted")?r.when():this.save({deleted:!0},e)},undelete:function(e){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},e)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name","tags"],toString:function(){var e=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+e.join(",")+")"}}),u=h.extend({collectionClass:c,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),f=h.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",e,")"].join("")}})),g=l.extend({model:f,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedPairDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",e,")"].join("")}})),v=g.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedListDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",e,")"].join("")}})),w=g.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),b=h.extend({collectionClass:w,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:b}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(60),i(17),i(7),i(80),i(8),i(98),i(6),i(95)],s=function(e,t,i,n,s,d,c){"use strict";function h(e,t){var i=e.toJSON(),n=m(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}});return n}var u="collections",p=a.View.extend(i.LoggableMixin).extend({_logNamespace:u,tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:o.template(['',"<%- element.name %>","",'"].join("")),select:function(e){this.$el.toggleClass("selected",e),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var e=this,t=this.$el.parent().width();this.$el.animate({"margin-right":t},"fast",function(){e.trigger("discard",{source:e}),e.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(e){e.stopPropagation(),this.select(e)},_clickName:function(e){e.stopPropagation(),e.preventDefault();var t=([c("Enter a new name for the element"),":\n(",c("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(c("Enter a new name for the element")+":",this.element.name));t&&(this.element.name=t,this.render())},_clickDiscard:function(e){e.stopPropagation(),this.discard()},_dragstart:function(e){e.originalEvent&&(e=e.originalEvent),e.dataTransfer.effectAllowed="move",e.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(e){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(e){this.$el.parent().trigger(e)},toString:function(){return"DatasetCollectionElementView()"}}),f=a.View.extend(i.LoggableMixin).extend(n.CollectionCreatorMixin).extend({_logNamespace:u,elementViewClass:p,collectionClass:e.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;o.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=o.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){if("dataset"!==e.history_content_type)return c("is not a dataset");var i=e.state===t.OK||o.contains(t.NOT_READY_STATES,e.state);return i?e.deleted||e.purged?c("has been deleted or purged"):null:c("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=900,t=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+t+")",t+=1,t>=e)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var i=this,n=l("
"),s=i.$list();o.each(this.elementViews,function(e){e.destroy(),i.removeElementView(e)}),i.workingElements.forEach(function(e){var t=i._createElementView(e);n.append(t.$el)}),i._renderClearSelected(),s.empty().append(n.children()),o.invoke(i.elementViews,"render"),s.height()>s.css("max-height")?s.css("border-width","1px 0px 1px 0px"):s.css("border-width","0px")},_createElementView:function(e){var t=new this.elementViewClass({element:e,selected:o.has(this.selectedIds,e.id)});return this.elementViews.push(t),this._listenToElementView(t),t},_listenToElementView:function(e){var t=this;t.listenTo(e,{select:function(e){var i=e.source.element;e.selected?t.selectedIds[i.id]=!0:delete t.selectedIds[i.id],t.trigger("elements:select",e)},discard:function(e){t.trigger("elements:discard",e)}})},addElementView:function(e){},removeElementView:function(e){delete this.selectedIds[e.element.id],this._renderClearSelected(),this.elementViews=o.without(this.elementViews,e),this.stopListening(e)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(e){return e},createList:function(e){if(!this.workingElements.length){var t=c("No valid elements for final list")+". ";return t+=''+c("Cancel")+" ",t+=c("or"),t+=' '+c("start over")+".",void this._showAlert(t)}var i=this,n=this.workingElements.map(function(e){return i._elementToJSON(e)});return i.blocking=!0,i.creationFn(n,e,i.hideOriginals).always(function(){i.blocking=!1}).fail(function(e,t,n){i.trigger("error",{xhr:e,status:t,message:c("An error occurred while creating this collection")})}).done(function(e,t,n){i.trigger("collection:created",e,t,n),i.metric("collection:created",e),"function"==typeof i.oncreate&&i.oncreate.call(this,e,t,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(e){this._renderClearSelected()}),this.on("elements:discard",function(e){var t=e.source.element;this.removeElementView(e.source),this.workingElements=o.without(this.workingElements,t),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(e){this.error(e);var t=this;if(content=e.message||c("An error occurred"),e.xhr){var i=e.xhr,n=e.message;0===i.readyState&&0===i.status?content+=": "+c("Galaxy could not be reached and may be updating.")+c(" Try again in a few minutes."):i.responseJSON?content+=":
"+JSON.stringify(i.responseJSON)+"
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e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(e,t){if(a.isBoolean(e)&&e!==this.includeDeleted){if(this.includeDeleted=e,a.result(t,"silent"))return;this.trigger("include-deleted",e,this)}},setIncludeHidden:function(e,t){if(a.isBoolean(e)&&e!==this.includeHidden){if(this.includeHidden=e,t=t||{},a.result(t,"silent"))return;this.trigger("include-hidden",e,this)}},fetch:function(e){if(e=e||{},this.historyId&&!e.details){var t=n.HistoryPrefs.get(this.historyId).toJSON();a.isEmpty(t.expandedIds)||(e.details=a.values(t.expandedIds).join(","))}return d.prototype.fetch.call(this,e)},_buildFetchData:function(e){return a.extend(d.prototype._buildFetchData.call(this,e),{v:"dev"})},_fetchParams:d.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(e){var t=d.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),a.defaults(t,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(e){e=e||{};var t=this;return e.filters=a.extend(e.filters,{deleted:!0,purged:void 0}),e.remove=!1,t.trigger("fetching-deleted",t),t.fetch(e).always(function(){t.trigger("fetching-deleted-done",t)})},fetchHidden:function(e){e=e||{};var t=this;return e.filters=a.extend(e.filters,{visible:!1}),e.remove=!1,t.trigger("fetching-hidden",t),t.fetch(e).always(function(){t.trigger("fetching-hidden-done",t)})},fetchAllDetails:function(e){e=e||{};var t={details:"all"};return e.data=a.extend(e.data||{},t),this.fetch(e)},fetchCollectionCounts:function(e){return e=e||{},e.keys=["type_id","element_count"].join(","),e.filters=a.extend(e.filters||{},{history_content_type:"dataset_collection"}),e.remove=!1,this.fetch(e)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var a=i.get(t[n]);return a?e.concat(a):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(e,t,i){return i=i||this.models,new l.AjaxQueue(i.slice().reverse().map(function(i,n){var s=a.isString(e)?i[e]:e;return function(){return s.apply(i,t)}})).deferred},progressivelyFetchDetails:function(e){function i(t){t=t||0;var o=a.extend(a.clone(e),{view:"summary",keys:d,limit:r,offset:t,reset:0===t,remove:!1});a.defer(function(){s.fetch.call(s,o).fail(n.reject).done(function(e){n.notify(e,r,t),e.length!==r?(s.allFetched=!0,n.resolve(e,r,t)):i(t+r)})})}e=e||{};var n=o.Deferred(),s=this,r=e.limitPerCall||s.limitPerProgressiveFetch,l=t.HistoryDatasetAssociation.prototype.searchAttributes,d=l.join(",");return i(),n},isCopyable:function(e){var t=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(e)&&e.id&&a.contains(t,e.model_class)},copy:function(e){var t,i,n;a.isString(e)?(t=e,n="hda",i="dataset"):(t=e.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[e.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,r=o.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:t,source:n,type:i})}).done(function(e){s.add([e],{parse:!0})}).fail(function(e,a,o){s.trigger("error",s,r,{},"Error copying contents",{type:i,id:t,source:n})});return r},createHDCA:function(e,t,i,n,s){var a=this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e});return a.save(s)},haveSearchDetails:function(){return this.allFetched&&this.all(function(e){return a.has(e.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=r.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(61),i(63),i(79),i(4),i(7),i(6)],s=function(e,t,i,n,s,d){"use strict";var c=a.Model.extend(s.LoggableMixin).extend(s.mixin(s.SearchableModelMixin,{_logNamespace:"history",UPDATE_DELAY:4e3,defaults:{model_class:"History",id:null,name:"Unnamed History",state:"new",deleted:!1,contents_active:{},contents_states:{}},urlRoot:Galaxy.root+"api/histories",contentsClass:e.HistoryContents,searchAttributes:["name","annotation","tags"],searchAliases:{title:"name",tag:"tags"},initialize:function(e,t){t=t||{},this.logger=t.logger||null,this.log(this+".initialize:",e,t),this.contents=new this.contentsClass([],{history:this,historyId:this.get("id"),order:t.order}),this._setUpListeners(),this._setUpCollectionListeners(),this.updateTimeoutId=null},_setUpListeners:function(){return this.on({error:function(e,t,i,n,s){this.clearUpdateTimeout()},"change:id":function(e,t){this.contents&&(this.contents.historyId=t)}})},_setUpCollectionListeners:function(){return this.contents?this.listenTo(this.contents,{error:function(){this.trigger.apply(this,o.makeArray(arguments))}}):this},contentsShown:function(){var e=this.get("contents_active"),t=e.active||0;return t+=this.contents.includeDeleted?e.deleted:0,t+=this.contents.includeHidden?e.hidden:0},nice_size:function(){var e=this.get("size");return e?n.bytesToString(e,!0,2):d("(empty)")},toJSON:function(){return r.extend(a.Model.prototype.toJSON.call(this),{nice_size:this.nice_size()})},get:function(e){return"nice_size"===e?this.nice_size():a.Model.prototype.get.apply(this,arguments)},ownedByCurrUser:function(){return!(!Galaxy||!Galaxy.user)&&(!Galaxy.user.isAnonymous()&&Galaxy.user.id===this.get("user_id"))},numOfUnfinishedJobs:function(){var e=this.get("non_ready_jobs");return e?e.length:0},numOfUnfinishedShownContents:function(){return this.contents.runningAndActive().length||0},_fetchContentRelatedAttributes:function(){var e=["size","non_ready_jobs","contents_active","hid_counter"];return this.fetch({data:l.param({keys:e.join(",")})})},refresh:function(e){e=e||{};var t=this,i=t.lastUpdateTime;this.contents.allFetched=!1;var n=0!==t.contents.currentPage?function(){return t.contents.fetchPage(t.contents.currentPage)}:function(){return t.contents.fetchUpdated(i)};return n().done(function(i,n,s){var a;try{a=new Date(s.getResponseHeader("Date"))}catch(e){}t.lastUpdateTime=a||new Date,t.checkForUpdates(e)})},checkForUpdates:function(e){function t(){n.clearUpdateTimeout(),n.updateTimeoutId=setTimeout(function(){n.refresh(e)},i)}e=e||{};var i=this.UPDATE_DELAY,n=this;if(n.id){var s=this.numOfUnfinishedShownContents();s>0?t():n._fetchContentRelatedAttributes().done(function(e){n.numOfUnfinishedJobs()>0?t():n.trigger("ready")})}},clearUpdateTimeout:function(){this.updateTimeoutId&&(clearTimeout(this.updateTimeoutId),this.updateTimeoutId=null)},parse:function(e,t){var i=a.Model.prototype.parse.call(this,e,t);return i.create_time&&(i.create_time=new Date(i.create_time)),i.update_time&&(i.update_time=new Date(i.update_time)),i},fetchWithContents:function(e,t){e=e||{};var i=this;return e.view="dev-detailed",this.fetch(e).then(function(e){return i.contents.history=i,i.contents.setHistoryId(e.id),i.fetchContents(t)})},fetchContents:function(e){e=e||{};var t=this;return t.lastUpdateTime=new Date,t.contents.fetchCurrentPage(e)},_delete:function(e){return this.get("deleted")?o.when():this.save({deleted:!0},e)},purge:function(e){return this.get("purged")?o.when():this.save({deleted:!0,purged:!0},e)},undelete:function(e){return this.get("deleted")?this.save({deleted:!1},e):o.when()},copy:function(e,t,i){if(e=void 0===e||e,!this.id)throw new Error("You must set the history ID before copying it.");var n={history_id:this.id};e&&(n.current=!0),t&&(n.name=t),i||(n.all_datasets=!1),n.view="dev-detailed";var s=this,a=o.post(this.urlRoot,n);return e?a.then(function(e){var t=new c(e);return t.setAsCurrent().done(function(){s.trigger("copied",s,e)})}):a.done(function(e){s.trigger("copied",s,e)})},setAsCurrent:function(){var e=this,t=o.getJSON(Galaxy.root+"history/set_as_current?id="+this.id);return t.done(function(){e.trigger("set-as-current",e)}),t},toString:function(){return"History("+this.get("id")+","+this.get("name")+")"}})),h=i.InfinitelyScrollingCollection,u=h.extend(s.LoggableMixin).extend({_logNamespace:"history",model:c,order:"update_time",limitOnFirstFetch:10,limitPerFetch:10,initialize:function(e,t){t=t||{},this.log("HistoryCollection.initialize",e,t),h.prototype.initialize.call(this,e,t),this.includeDeleted=t.includeDeleted||!1,this.currentHistoryId=t.currentHistoryId,this.setUpListeners()},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot},setUpListeners:function(){return this.on({"change:deleted":function(e){this.debug("change:deleted",this.includeDeleted,e.get("deleted")),!this.includeDeleted&&e.get("deleted")&&this.remove(e)},copied:function(e,t){this.setCurrent(new c(t,[]))},"set-as-current":function(e){var t=this.currentHistoryId;this.trigger("no-longer-current",t),this.currentHistoryId=e.id}})},_buildFetchData:function(e){return r.extend(h.prototype._buildFetchData.call(this,e),{view:"dev-detailed"})},_buildFetchFilters:function(e){var t=h.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted?i.deleted=null:(i.deleted=!1,i.purged=!1),r.defaults(t,i)},fetchFirst:function(e){var t=this,i=l.when();return this.currentHistoryId&&(i=h.prototype.fetchFirst.call(t,{silent:!0,limit:1,filters:{purged:"",deleted:"","encoded_id-in":this.currentHistoryId}})),i.then(function(){return e=e||{},e.offset=0,t.fetchMore(e)})},comparators:r.extend(r.clone(h.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),size:s.buildComparator("size",{ascending:!1}),"size-asc":s.buildComparator("size",{ascending:!0})}),sort:function(e){e=e||{};var t=e.silent,i=this.remove(this.get(this.currentHistoryId));return h.prototype.sort.call(this,r.defaults({silent:!0},e)),this.unshift(i,{silent:!0}),t||this.trigger("sort",this,e),this},create:function(e,t,i,n){var s=this,a=o.getJSON(Galaxy.root+"history/create_new_current");return a.done(function(e){s.setCurrent(new c(e,[],i||{}))})},setCurrent:function(e,t){return t=t||{},this.unshift(e,t),this.currentHistoryId=e.get("id"),t.silent||this.trigger("new-current",e,this),this},toString:function(){return"HistoryCollection("+this.length+",current:"+this.currentHistoryId+")"}});return{History:c,HistoryCollection:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3),i(1))},function(e,t,i){var n,s;(function(a){n=[i(7)],s=function(e){"use strict";var t=e.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(e){return a.result(this.get("expandedIds"),e,!1)},allExpanded:function(){return a.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(e){return a.isUndefined(e)||this.set("show_deleted",e),this.get("show_deleted")},includeHidden:function(e){return a.isUndefined(e)||this.set("show_hidden",e),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return t.storageKeyPrefix+e},get:function(e){return new t({id:t.historyStorageKey(e)})},clearAll:function(e){for(var i in sessionStorage)0===i.indexOf(t.storageKeyPrefix)&&sessionStorage.removeItem(i)}});return{HistoryPrefs:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3))},function(e,t,i){var n,s;(function(a,o,r,l){n=[i(7),i(6)],s=function(e,t){"use strict";var i="list",n=a.View.extend(e.LoggableMixin).extend({_logNamespace:i,initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded),this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=o(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):o(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=o(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}}),s=n.extend(e.mixin(e.SelectableViewMixin,e.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(t){n.prototype.initialize.call(this,t),e.SelectableViewMixin.initialize.call(this,t),e.DraggableViewMixin.initialize.call(this,t),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=n.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return n.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=o('
    '),i=e.model.toJSON();return r.each(e.templates.warnings,function(n){t.append(o(n(i,e)))}),t},_renderTitleBar:function(){return o(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return o(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){var t=32,i=13;return!e||"keydown"!==e.type||e.keyCode!==t&&e.keyCode!==i||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){var e=this.model?this.model+"":"(no model)";return"ListItemView("+e+")"}}));s.prototype.templates=function(){var t=e.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=e.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=e.wrapTemplate(['
    ']),a=e.wrapTemplate(['
    ']);return{el:t,warnings:i,titleBar:n,subtitle:s,details:a}}();var d=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return o();var e=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e),n=new t(r.extend(i,{model:e}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});return d.prototype.templates=function(){var t=e.wrapTemplate(['
    ',"
    "],"collection"); -return r.extend({},s.prototype.templates,{details:t})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3),i(1))},function(e,t,i){var n,s;(function(a,o){n=[i(7),i(6)],s=function(e,t){var i=a.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(e){e.usePrompt===!1?this.label="":this.label='",this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_template:function(){return[this.label,''].join("")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!o.isArray(t)||o.isEmpty(t)?"":t.map(function(t){return o.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return o.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=o.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(t.added.text+"")})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");o.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),a.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3))},function(e,t,i){var n,s;(function(a,o){n=[i(3),i(27),i(16),i(44)],s=function(e,t,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},r=a.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(e){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new r(this.toJSON())},set_value:function(e){this.set("value",e||"")}}),l=a.Collection.extend({model:r}),d=r.extend({}),c=r.extend({set_value:function(e){this.set("value",parseInt(e,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=c.extend({set_value:function(e){this.set("value",parseFloat(e))}}),u=r.extend({get_samples:function(){return e.map(this.get("options"),function(e){return e[0]})}});r.subModelTypes={integer:c,float:h,data:d,select:u};var p=a.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(t){this.set("inputs",new l(e.map(t.inputs,function(e){var t=r.subModelTypes[e.type]||r;return new t(e)})))},toJSON:function(){var e=a.Model.prototype.toJSON.call(this);return e.inputs=this.get("inputs").map(function(e){return e.toJSON()}),e},remove_inputs:function(e){var t=this,i=t.get("inputs").filter(function(t){return e.indexOf(t.get("type"))!==-1});t.get("inputs").remove(i)},copy:function(e){var t=new p(this.toJSON());if(e){var i=new a.Collection;t.get("inputs").each(function(e){e.get_samples()&&i.push(e)}),t.set("inputs",i)}return t},apply_search_results:function(t){return e.indexOf(t,this.attributes.id)!==-1?this.show():this.hide(),this.is_visible()},set_input_value:function(e,t){this.get("inputs").find(function(t){return t.get("name")===e}).set("value",t)},set_input_values:function(t){var i=this;e.each(e.keys(t),function(e){i.set_input_value(e,t[e])})},run:function(){return this._run()},rerun:function(e,t){return this._run({action:"rerun",target_dataset_id:e.id,regions:t})},get_inputs_dict:function(){var e={};return this.get("inputs").each(function(t){e[t.get("name")]=t.get("value")}),e},_run:function(n){var s=e.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),a=o.Deferred(),r=new t.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});return o.when(r.go()).then(function(e){a.resolve(new i.DatasetCollection(e))}),a}});e.extend(p.prototype,s);var f=(a.View.extend({}),a.Collection.extend({model:p})),g=a.Model.extend(s),m=a.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){e.each(this.attributes.elems,function(e){e.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var i,n=!0;e.each(this.attributes.elems,function(e){e instanceof g?(i=e,i.hide()):e instanceof p&&e.apply_search_results(t)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});e.extend(m.prototype,s);var v=a.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var e=this.attributes.query;if(e.length");e.append(E.tool_link(this.model.toJSON()));var t=this.model.get("form_style",null);if("upload1"===this.model.id)e.find("a").on("click",function(e){e.preventDefault(),Galaxy.upload.show()});else if("regular"===t){var i=this;e.find("a").on("click",function(e){e.preventDefault(),Galaxy.router.push("/",{tool_id:i.model.id,version:i.model.get("version")})})}return this.$el.append(e),this}}),b=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(o("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(E.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return e.each(this.model.attributes.elems,function(e){if(e instanceof p){var i=new w({model:e,className:"toolTitle"});i.render(),t.append(i.$el)}else if(e instanceof g){var n=new b({model:e});n.render(),t.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=a.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","change :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(E.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),o("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(e){return this.model.attributes.clear_key&&this.model.attributes.clear_key===e.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=a.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new C({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof m){var i=new x({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof p){var n=new w({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof g){var s=new b({model:t});s.render(),e.$el.append(s.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=o(this).attr("class").split(/\s+/)[0],n=e.model.get("tools").get(i);e.trigger("tool_link_click",t,n)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?o("#search-no-results").show():o("#search-no-results").hide()}}),k=a.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(E.tool_form(this.model.toJSON()))}}),E=(a.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new k},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),o("#left").width("650px")})}}),{tool_search:e.template(['',' ',''].join("")),panel_section:e.template(['
    ','<%- name %>',"
    ",'