',
+ _l( 'There was an error getting the data for this collection' ), ': <%- model.error %>',
+ '
',
+ '<% } %>'
+ ]),
+ purged : BASE_MVC.wrapTemplate([
+ '<% if( model.purged ){ %>',
+ '',
+ _l( 'This collection has been deleted and removed from disk' ),
+ '
',
+ '<% } %>'
+ ]),
+ deleted : BASE_MVC.wrapTemplate([
+ // deleted not purged
+ '<% if( model.deleted && !model.purged ){ %>',
+ '',
+ _l( 'This collection has been deleted' ),
+ '
',
+ '<% } %>'
+ ])
+ });
+
// use element identifier
var titleBarTemplate = BASE_MVC.wrapTemplate([
'',
@@ -85,6 +122,7 @@ DCListItemView.prototype.templates = (function(){
], 'collection' );
return _.extend( {}, FoldoutListItemView.prototype.templates, {
+ warnings : warnings,
titleBar : titleBarTemplate
});
}());
diff --git a/client/galaxy/scripts/mvc/collection/list-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
new file mode 100644
index 00000000000..af2b795223c
--- /dev/null
+++ b/client/galaxy/scripts/mvc/collection/list-collection-creator.js
@@ -0,0 +1,52 @@
+define([
+ "mvc/dataset/states",
+ "mvc/ui/error-modal",
+ "utils/localization"
+], function( STATES, errorModal, _l ){
+/*==============================================================================
+
+==============================================================================*/
+function validElements( collection ){
+ var elements = collection.toJSON().filter( function( content ){
+ return content.history_content_type === 'dataset'
+ && content.state === STATES.OK;
+ });
+ return elements;
+}
+
+var noValidElementsMessage = 'No valid datasets were selected';
+
+function noValidElementsErrorModal(){
+ errorModal(
+ 'Use the checkboxes at the left of the dataset names to select them. ' +
+ 'Selected datasets should be error-free and should have completed running.',
+ noValidElementsMessage
+ );
+}
+
+function createListHDCA( collection ){
+ var name = 'New Dataset List',
+ elementIdentifiers = validElements( collection ).map( function( element ){
+ // TODO: Handle duplicate names.
+ return {
+ id : element.id,
+ name : element.name,
+ //TODO: this allows for list:list even if the filter above does not - reconcile
+ src : ( element.history_content_type === 'dataset'? 'hda' : 'hdca' )
+ }
+ });
+ if( !elementIdentifiers.length ){
+ noValidElementsErrorModal();
+ return jQuery.Deferred().reject( noValidElementsMessage );
+ }
+ return collection.createHDCA( elementIdentifiers, 'list', name );
+}
+
+//==============================================================================
+ return {
+ validElements : validElements,
+ noValidElementsMessage : noValidElementsMessage,
+ noValidElementsErrorModal : noValidElementsErrorModal,
+ createListHDCA : createListHDCA
+ };
+});
diff --git a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
similarity index 98%
rename from client/galaxy/scripts/mvc/collection/paired-collection-creator.js
rename to client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
index f956c1f43a4..b5ac964eb02 100644
--- a/client/galaxy/scripts/mvc/collection/paired-collection-creator.js
+++ b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
@@ -1,9 +1,10 @@
define([
"utils/levenshtein",
"utils/natural-sort",
+ "mvc/collection/list-collection-creator",
"mvc/base-mvc",
"utils/localization"
-], function( levenshteinDistance, naturalSort, baseMVC, _l ){
+], function( levenshteinDistance, naturalSort, LIST_COLLECTION_CREATOR, baseMVC, _l ){
/* ============================================================================
TODO:
@@ -247,6 +248,9 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
/** DOM elements currently being dragged */
this.$dragging = null;
+ /** Used for blocking UI events during ajax/operations (don't post twice) */
+ this.blocking = false;
+
this._setUpBehaviors();
this._dataSetUp();
},
@@ -576,12 +580,16 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
};
//this.debug( JSON.stringify( ajaxData ) );
+ creator.blocking = true;
return jQuery.ajax( url, {
type : 'POST',
contentType : 'application/json',
dataType : 'json',
data : JSON.stringify( ajaxData )
})
+ .always( function(){
+ creator.blocking = false;
+ })
.fail( function( xhr, status, message ){
creator._ajaxErrHandler( xhr, status, message );
})
@@ -855,7 +863,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
what.addClass( VALIDATION_CLASS );
}
},
-
+
// ------------------------------------------------------------------------ events
/** set up event handlers on self */
_setUpBehaviors : function(){
@@ -1406,7 +1414,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
/** check for enter key press when in the collection name and submit */
_nameCheckForEnter : function( ev ){
- if( ev.keyCode === 13 ){
+ if( ev.keyCode === 13 && !this.blocking ){
this._clickCreate();
}
},
@@ -1421,7 +1429,7 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
var name = this._getName();
if( !name ){
this._validationWarning( 'name' );
- } else {
+ } else if( !this.blocking ){
this.createList();
}
},
@@ -1683,12 +1691,18 @@ PairedCollectionCreator.templates = PairedCollectionCreator.templates || {
/** a modal version of the paired collection creator */
var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datasets, options ){
+ var deferred = jQuery.Deferred(),
+ creator;
+
options = _.defaults( options || {}, {
datasets : datasets,
- oncancel : function(){ Galaxy.modal.hide(); },
- oncreate : function(){
+ oncancel : function(){
Galaxy.modal.hide();
- Galaxy.currHistoryPanel.refreshContents();
+ deferred.reject( 'cancelled' );
+ },
+ oncreate : function( creator, response ){
+ Galaxy.modal.hide();
+ deferred.resolve( response );
}
});
@@ -1696,7 +1710,7 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datas
throw new Error( 'Galaxy or Galaxy.modal not found' );
}
- var creator = new PairedCollectionCreator( options );
+ creator = new PairedCollectionCreator( options );
Galaxy.modal.show({
title : 'Create a collection of paired datasets',
body : creator.$el,
@@ -1705,15 +1719,31 @@ var pairedCollectionCreatorModal = function _pairedCollectionCreatorModal( datas
closing_events: true
});
creator.render();
+ window.creator = creator;
+
//TODO: remove modal header
- window.PCC = creator;
- return creator;
+ return deferred;
};
+//=============================================================================
+function createListOfPairsCollection( collection ){
+ var elements = LIST_COLLECTION_CREATOR.validElements( collection );
+ if( !elements.length ){
+ LIST_COLLECTION_CREATOR.noValidElementsErrorModal();
+ return jQuery.Deferred().reject( LIST_COLLECTION_CREATOR.noValidElementsMessage );
+ }
+
+ return pairedCollectionCreatorModal( elements, {
+ historyId : collection.historyId
+ });
+}
+
+
//=============================================================================
return {
PairedCollectionCreator : PairedCollectionCreator,
- pairedCollectionCreatorModal : pairedCollectionCreatorModal
+ pairedCollectionCreatorModal : pairedCollectionCreatorModal,
+ createListOfPairsCollection : createListOfPairsCollection
};
});
diff --git a/client/galaxy/scripts/mvc/collection/pair-collection-creator.js b/client/galaxy/scripts/mvc/collection/pair-collection-creator.js
new file mode 100644
index 00000000000..99185221382
--- /dev/null
+++ b/client/galaxy/scripts/mvc/collection/pair-collection-creator.js
@@ -0,0 +1,33 @@
+define([
+ "mvc/collection/list-collection-creator",
+ "mvc/ui/error-modal",
+ "utils/localization"
+], function( LIST_COLLECTION_CREATOR, errorModal, _l ){
+
+ function createPairHDCA( collection ){
+ // currently: datasets in the ok state
+ var elementsJSON = LIST_COLLECTION_CREATOR.validElements( collection );
+ if( !elementsJSON.length ){
+ LIST_COLLECTION_CREATOR.noValidElementsErrorModal();
+ return jQuery.Deferred().reject( LIST_COLLECTION_CREATOR.noValidElementsMessage );
+ }
+ if( elementsJSON.length !== 2 ){
+ errorModal(
+ 'When pairing datasets, select only two datasets: one forward and one reverse.',
+ 'Not a valid pair'
+ );
+ return jQuery.Deferred().reject( LIST_COLLECTION_CREATOR.noValidElementsMessage );
+ }
+
+ var name = 'New Dataset Pair',
+ elementIdentifiers = [
+ { name: "forward", src: "hda", id: elementsJSON[0].id },
+ { name: "reverse", src: "hda", id: elementsJSON[1].id }
+ ];
+ return collection.createHDCA( elementIdentifiers, 'paired', name );
+ }
+
+ return {
+ createPairHDCA : createPairHDCA
+ };
+});
diff --git a/client/galaxy/scripts/mvc/history/hdca-li.js b/client/galaxy/scripts/mvc/history/hdca-li.js
index e8c744f359c..ee633d82e87 100644
--- a/client/galaxy/scripts/mvc/history/hdca-li.js
+++ b/client/galaxy/scripts/mvc/history/hdca-li.js
@@ -18,6 +18,17 @@ var HDCAListItemView = _super.extend(
className : _super.prototype.className + " history-content",
+ /** event listeners */
+ _setUpListeners : function(){
+ _super.prototype._setUpListeners.call( this );
+ // re-rendering on deletion
+ this.model.on( 'change', function( model, options ){
+ if( _.isEqual( _.keys( model.changed ), [ 'visible' ] ) ){
+ this.render();
+ }
+ }, this );
+ },
+
/** Override to provide the proper collections panels as the foldout */
_getFoldoutPanelClass : function(){
switch( this.model.get( 'collection_type' ) ){
@@ -53,6 +64,17 @@ var HDCAListItemView = _super.extend(
/** underscore templates */
HDCAListItemView.prototype.templates = (function(){
+ var warnings = _.extend( {}, _super.prototype.templates.warnings, {
+ hidden : BASE_MVC.wrapTemplate([
+ // add a warning when hidden
+ '<% if( !collection.visible ){ %>',
+ '
',
+ _l( 'This collection has been hidden' ),
+ '
',
+ '<% } %>'
+ ], 'collection' )
+ });
+
// could steal this from hda-base (or use mixed content)
var titleBarTemplate = BASE_MVC.wrapTemplate([
// adding the hid display to the title
@@ -68,6 +90,7 @@ HDCAListItemView.prototype.templates = (function(){
], 'collection' );
return _.extend( {}, _super.prototype.templates, {
+ warnings : warnings,
titleBar : titleBarTemplate
});
}());
diff --git a/client/galaxy/scripts/mvc/history/history-contents.js b/client/galaxy/scripts/mvc/history/history-contents.js
index acdbaa6f48e..165f5ff41a6 100644
--- a/client/galaxy/scripts/mvc/history/history-contents.js
+++ b/client/galaxy/scripts/mvc/history/history-contents.js
@@ -220,12 +220,12 @@ var HistoryContents = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).exten
source : contentType,
type : type
})
- .done( function( json ){
- collection.add([ json ]);
+ .done( function( response ){
+ collection.add([ response ]);
})
.fail( function( error, status, message ){
collection.trigger( 'error', collection, xhr, {},
- 'Error copying contents', { type: type, id: id, source: contentType });
+ 'Error copying contents', { type: type, id: id, source: contentType });
});
return xhr;
},
diff --git a/client/galaxy/scripts/mvc/history/history-panel-edit.js b/client/galaxy/scripts/mvc/history/history-panel-edit.js
index bf7d1fa23c2..ae1de05ef56 100644
--- a/client/galaxy/scripts/mvc/history/history-panel-edit.js
+++ b/client/galaxy/scripts/mvc/history/history-panel-edit.js
@@ -7,6 +7,9 @@ define([
"mvc/history/hdca-li-edit",
"mvc/tags",
"mvc/annotations",
+ "mvc/collection/list-collection-creator",
+ "mvc/collection/pair-collection-creator",
+ "mvc/collection/list-of-pairs-collection-creator",
"ui/fa-icon-button",
"mvc/ui/popup-menu",
"utils/localization"
@@ -19,6 +22,9 @@ define([
HDCA_LI_EDIT,
TAGS,
ANNOTATIONS,
+ LIST_COLLECTION_CREATOR,
+ PAIR_COLLECTION_CREATOR,
+ LIST_OF_PAIRS_COLLECTION_CREATOR,
faIconButton,
PopupMenu,
_l
@@ -27,63 +33,6 @@ define([
TODO:
============================================================================= */
-function createListCollection( history, collection ){
- //TODO: filter out non-datasets, non-ready
- //TODO: fail if no valid elements remain
- //return jQuery.Deferred().reject( _l( 'No valid datasets to add' ) );
- var name = 'New Dataset List',
- elementIdentifiers = collection.toJSON().map( function( element ){
- // TODO: Handle duplicate names.
- return {
- id : element.id,
- name : element.name,
- src : ( element.history_content_type === 'dataset'? 'hda' : 'hdca' )
- }
- });
- return collection.createHDCA( elementIdentifiers, 'list', name );
-}
-
-function createPairCollection( history, collection ){
- //TODO: filter out non-datasets, non-ready
- //TODO: fail if no valid elements remain
- //return jQuery.Deferred().reject( _l( 'No valid datasets to add' ) );
- var elementsJSON = collection.toJSON(),
- name = 'New Dataset Pair',
- elementIdentifiers = [
- { name: "forward", src: "hda", id: elementsJSON[0].id },
- { name: "reverse", src: "hda", id: elementsJSON[1].id }
- ];
- return collection.createHDCA( elementIdentifiers, 'paired', name );
-}
-
-function createListOfPairsCollection( history, collection ){
- var datasets = collection.toJSON().filter( function( content ){
- return content.history_content_type === 'dataset'
- && content.state === STATES.OK;
- });
-
- if( datasets.length ){
- require([ 'mvc/collection/paired-collection-creator' ], function( creator ){
- window.creator = creator.pairedCollectionCreatorModal( datasets, {
- historyId : history.id
- });
- });
-
- } else {
- Galaxy.modal.show({
- title : _l( 'No valid datasets were selected' ),
- body : _l([
- 'Use the checkboxes at the left of the dataset names to select them.',
- 'Selected datasets should be error-free and should have completed running.'
- ].join(' ')),
- buttons : { 'Ok': function(){ Galaxy.modal.hide(); } },
- closing_events: true
- });
- }
-}
-
-
-// =============================================================================
var _super = HPANEL.HistoryPanel;
// base class for current-history-panel and used as-is in history/view.mako
/** @class Editable View/Controller for the history model.
@@ -329,23 +278,31 @@ var HistoryPanelEdit = _super.extend(
}
});
}
- return actions.concat([
+ actions = actions.concat( panel._collectionActions() );
+ return actions;
+ },
+
+ /** */
+ _collectionActions : function(){
+ var panel = this;
+ return [
{ html: _l( 'Build Dataset List' ), func: function() {
- createListCollection( panel.model, panel.getSelectedModels() )
+ LIST_COLLECTION_CREATOR.createListHDCA( panel.getSelectedModels() )
.done( function(){ panel.model.refresh() });
}
},
// TODO: Only show quick pair if two things selected.
{ html: _l( 'Build Dataset Pair' ), func: function() {
- createPairCollection( panel.model, panel.getSelectedModels() )
+ PAIR_COLLECTION_CREATOR.createPairHDCA( panel.getSelectedModels() )
.done( function(){ panel.model.refresh() });
}
},
{ html: _l( 'Build List of Dataset Pairs' ), func: function() {
- createListOfPairsCollection( panel.model, panel.getSelectedModels() );
+ LIST_OF_PAIRS_COLLECTION_CREATOR.createListOfPairsCollection( panel.getSelectedModels() )
+ .done( function(){ panel.model.refresh() });
}
},
- ]);
+ ];
},
// ------------------------------------------------------------------------ sub-views
diff --git a/client/galaxy/scripts/mvc/ui/error-modal.js b/client/galaxy/scripts/mvc/ui/error-modal.js
new file mode 100644
index 00000000000..379b62af9e4
--- /dev/null
+++ b/client/galaxy/scripts/mvc/ui/error-modal.js
@@ -0,0 +1,29 @@
+define([
+ "utils/localization"
+], function( _l ){
+
+ function _errorModal( message, title ){
+ Galaxy.modal.show({
+ title : _l( title ),
+ body : _l( message ),
+ buttons : { 'Ok': function(){ Galaxy.modal.hide(); } },
+ closing_events: true
+ });
+ }
+
+ function _errorAlert( message, title ){
+ alert( title + '\n\n' + message );
+ }
+
+ function errorModal( message, title ){
+ if( !message ){ return; }
+ title = title || 'Error';
+ if( window.Galaxy && Galaxy.modal ){
+ return _errorModal( message, title );
+ }
+ return _errorAlert( message, title );
+ }
+
+
+return errorModal;
+});
diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
index fb12faf78aa..c50f69d5827 100644
--- a/lib/galaxy/managers/histories.py
+++ b/lib/galaxy/managers/histories.py
@@ -283,23 +283,24 @@ class HistorySerializer( sharable.SharableModelSerializer, deletable.PurgableSer
deletable.PurgableSerializerMixin.add_serializers( self )
self.serializers.update({
- 'model_class': lambda *a: 'History',
- 'id': self.serialize_id,
- 'create_time': self.serialize_date,
- 'update_time': self.serialize_date,
- 'size': lambda t, i, k: int( i.get_disk_size() ),
- 'nice_size': lambda t, i, k: i.get_disk_size( nice_size=True ),
- 'state': lambda t, i, k: self.history_manager.get_history_state( t, i ),
+ 'model_class' : lambda *a: 'History',
+ 'id' : self.serialize_id,
+ 'create_time' : self.serialize_date,
+ 'update_time' : self.serialize_date,
+ 'size' : lambda t, i, k: int( i.get_disk_size() ),
+ 'nice_size' : lambda t, i, k: i.get_disk_size( nice_size=True ),
+ 'state' : lambda t, i, k: self.history_manager.get_history_state( t, i ),
- 'url': lambda t, i, k: self.url_for( 'history', id=t.security.encode_id( i.id ) ),
- 'contents_url': lambda t, i, k: self.url_for( 'history_contents', history_id=t.security.encode_id( i.id ) ),
+ 'url' : lambda t, i, k: self.url_for( 'history', id=t.security.encode_id( i.id ) ),
+ 'contents_url' : lambda t, i, k: self.url_for( 'history_contents',
+ history_id=t.security.encode_id( i.id ) ),
- 'empty': lambda t, i, k: len( i.datasets ) <= 0,
- 'count': lambda trans, item, key: len( item.datasets ),
- 'hdas': lambda t, i, k: [ t.security.encode_id( hda.id ) for hda in i.datasets ],
- 'state_details': lambda t, i, k: self.history_manager.get_state_counts( t, i ),
- 'state_ids': lambda t, i, k: self.history_manager.get_state_ids( t, i ),
- 'contents': self.serialize_contents
+ 'empty' : lambda t, i, k: ( len( i.datasets ) + len( i.dataset_collections ) ) <= 0,
+ 'count' : lambda trans, item, key: len( item.datasets ),
+ 'hdas' : lambda t, i, k: [ t.security.encode_id( hda.id ) for hda in i.datasets ],
+ 'state_details' : lambda t, i, k: self.history_manager.get_state_counts( t, i ),
+ 'state_ids' : lambda t, i, k: self.history_manager.get_state_ids( t, i ),
+ 'contents' : self.serialize_contents
})
def serialize_contents( self, trans, history, *args ):
diff --git a/static/maps/mvc/collection/collection-li.js.map b/static/maps/mvc/collection/collection-li.js.map
index f3d1dac2123..1a99a58cf88 100644
--- a/static/maps/mvc/collection/collection-li.js.map
+++ b/static/maps/mvc/collection/collection-li.js.map
@@ -1 +1 @@
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diff --git a/static/maps/mvc/collection/list-collection-creator.js.map b/static/maps/mvc/collection/list-collection-creator.js.map
new file mode 100644
index 00000000000..f4ca81f06d8
--- /dev/null
+++ b/static/maps/mvc/collection/list-collection-creator.js.map
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
new file mode 100644
index 00000000000..2ac61225a5a
--- /dev/null
+++ b/static/maps/mvc/collection/list-of-pairs-collection-creator.js.map
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/static/maps/mvc/collection/pair-collection-creator.js.map b/static/maps/mvc/collection/pair-collection-creator.js.map
new file mode 100644
index 00000000000..f5f16aea6fa
--- /dev/null
+++ b/static/maps/mvc/collection/pair-collection-creator.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"pair-collection-creator.js","sources":["../../../src/mvc/collection/pair-collection-creator.js"],"names":["define","LIST_COLLECTION_CREATOR","errorModal","createPairHDCA","collection","elementsJSON","validElements","length","noValidElementsErrorModal","jQuery","Deferred","reject","noValidElementsMessage","name","elementIdentifiers","src","id","createHDCA"],"mappings":"AAAAA,QACI,yCACA,qBACA,sBACD,SAAUC,EAAyBC,GAElC,QAASC,GAAgBC,GAErB,GAAIC,GAAeJ,EAAwBK,cAAeF,EAC1D,KAAKC,EAAaE,OAEd,MADAN,GAAwBO,4BACjBC,OAAOC,WAAWC,OAAQV,EAAwBW,uBAE7D,IAA4B,IAAxBP,EAAaE,OAKb,MAJAL,GACI,gFACA,oBAEGO,OAAOC,WAAWC,OAAQV,EAAwBW,uBAG7D,IAAIC,GAAO,mBACPC,IACMD,KAAM,UAAWE,IAAK,MAAOC,GAAIX,EAAa,GAAGW,KACjDH,KAAM,UAAWE,IAAK,MAAOC,GAAIX,EAAa,GAAGW,IAE3D,OAAOZ,GAAWa,WAAYH,EAAoB,SAAUD,GAGhE,OACIV,eAAiBA"}
\ No newline at end of file
diff --git a/static/maps/mvc/history/hdca-li.js.map b/static/maps/mvc/history/hdca-li.js.map
index 65e5a6ab84c..c7e5846127f 100644
--- a/static/maps/mvc/history/hdca-li.js.map
+++ b/static/maps/mvc/history/hdca-li.js.map
@@ -1 +1 @@
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index d73ec4288f5..7ceee9929f7 100644
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diff --git a/static/maps/mvc/history/history-panel-edit.js.map b/static/maps/mvc/history/history-panel-edit.js.map
index a93cc930e55..dc92a2a1a8b 100644
--- a/static/maps/mvc/history/history-panel-edit.js.map
+++ b/static/maps/mvc/history/history-panel-edit.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/static/maps/mvc/ui/error-modal.js.map b/static/maps/mvc/ui/error-modal.js.map
new file mode 100644
index 00000000000..819075abed9
--- /dev/null
+++ b/static/maps/mvc/ui/error-modal.js.map
@@ -0,0 +1 @@
+{"version":3,"file":"error-modal.js","sources":["../../../src/mvc/ui/error-modal.js"],"names":["define","_l","_errorModal","message","title","Galaxy","modal","show","body","buttons","Ok","hide","closing_events","_errorAlert","alert","errorModal","window"],"mappings":"AAAAA,QACI,sBACD,SAAUC,GAET,QAASC,GAAaC,EAASC,GAC3BC,OAAOC,MAAMC,MACTH,MAAUH,EAAIG,GACdI,KAAUP,EAAIE,GACdM,SAAYC,GAAM,WAAYL,OAAOC,MAAMK,SAC3CC,gBAAgB,IAIxB,QAASC,GAAaV,EAASC,GAC3BU,MAAOV,EAAQ,OAASD,GAG5B,QAASY,GAAYZ,EAASC,GAC1B,MAAKD,IACLC,EAAQA,GAAS,QACbY,OAAOX,QAAUA,OAAOC,MACjBJ,EAAaC,EAASC,GAE1BS,EAAaV,EAASC,IAL7B,OASR,MAAOW"}
\ No newline at end of file
diff --git a/static/scripts/mvc/collection/collection-li.js b/static/scripts/mvc/collection/collection-li.js
index 9f43c44b307..3afc7e84b05 100644
--- a/static/scripts/mvc/collection/collection-li.js
+++ b/static/scripts/mvc/collection/collection-li.js
@@ -1,2 +1,2 @@
-define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=a.FoldoutListItemView,f=a.ListItemView,g=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(a){this.linkTarget=a.linkTarget||"_blank",this.hasUser=a.hasUser,e.prototype.initialize.call(this,a)},_renderSubtitle:function(){var a=$('
');switch(this.model.get("collection_type")){case"list":return a.text(d("a list of datasets"));case"paired":return a.text(d("a pair of datasets"));case"list:paired":return a.text(d("a list of paired datasets"))}return a},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCListItemView("+a+")"}});g.prototype.templates=function(){var a=c.wrapTemplate(['
','
','<%- collection.element_identifier || collection.name %>',"
",'
',"
"],"collection");return _.extend({},e.prototype.templates,{titleBar:a})}();var h=f.extend({className:f.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DCEListItemView.initialize:",a),f.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCEListItemView("+a+")"}});h.prototype.templates=function(){var a=c.wrapTemplate(['
','
','<%- element.element_identifier %>',"
",'
',"
"],"element");return _.extend({},f.prototype.templates,{titleBar:a})}();var i=b.DatasetListItemView.extend({className:b.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DatasetDCEListItemView.initialize:",a),b.DatasetListItemView.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+a+")"}});i.prototype.templates=function(){var a=c.wrapTemplate(['
','
','
','<%- element.element_identifier %>',"
","
"],"element");return _.extend({},b.DatasetListItemView.prototype.templates,{titleBar:a})}();var j=g.extend({className:g.prototype.className+" dataset-collection-element",_swapNewRender:function(a){g.prototype._swapNewRender.call(this,a);var b=this.model.get("state")||"ok";return this.$el.addClass("state-"+b),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+a+")"}});return{DCListItemView:g,DCEListItemView:h,DatasetDCEListItemView:i,NestedDCDCEListItemView:j}});
+define(["mvc/list/list-item","mvc/dataset/dataset-li","mvc/base-mvc","utils/localization"],function(a,b,c,d){var e=a.FoldoutListItemView,f=a.ListItemView,g=e.extend({className:e.prototype.className+" dataset-collection",id:function(){return["dataset_collection",this.model.get("id")].join("-")},initialize:function(a){this.linkTarget=a.linkTarget||"_blank",this.hasUser=a.hasUser,e.prototype.initialize.call(this,a)},_setUpListeners:function(){e.prototype._setUpListeners.call(this),this.model.on("change",function(a){_.isEqual(_.keys(a.changed),["deleted"])&&this.render()},this)},_renderSubtitle:function(){var a=$('
');switch(this.model.get("collection_type")){case"list":return a.text(d("a list of datasets"));case"paired":return a.text(d("a pair of datasets"));case"list:paired":return a.text(d("a list of paired datasets"))}return a},_getFoldoutPanelOptions:function(){var a=e.prototype._getFoldoutPanelOptions.call(this);return _.extend(a,{linkTarget:this.linkTarget,hasUser:this.hasUser})},$selector:function(){return this.$("> .selector")},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCListItemView("+a+")"}});g.prototype.templates=function(){var a=_.extend({},e.prototype.templates.warnings,{error:c.wrapTemplate(["<% if( model.error ){ %>",'
',d("There was an error getting the data for this collection"),": <%- model.error %>","
","<% } %>"]),purged:c.wrapTemplate(["<% if( model.purged ){ %>",'
',d("This collection has been deleted and removed from disk"),"
","<% } %>"]),deleted:c.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
',d("This collection has been deleted"),"
","<% } %>"])}),b=c.wrapTemplate(['
','
','<%- collection.element_identifier || collection.name %>',"
",'
',"
"],"collection");return _.extend({},e.prototype.templates,{warnings:a,titleBar:b})}();var h=f.extend({className:f.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DCEListItemView.initialize:",a),f.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DCEListItemView("+a+")"}});h.prototype.templates=function(){var a=c.wrapTemplate(['
','
','<%- element.element_identifier %>',"
",'
',"
"],"element");return _.extend({},f.prototype.templates,{titleBar:a})}();var i=b.DatasetListItemView.extend({className:b.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(a){a.logger&&(this.logger=this.model.logger=a.logger),this.log("DatasetDCEListItemView.initialize:",a),b.DatasetListItemView.prototype.initialize.call(this,a)},toString:function(){var a=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+a+")"}});i.prototype.templates=function(){var a=c.wrapTemplate(['
','
','
','<%- element.element_identifier %>',"
","
"],"element");return _.extend({},b.DatasetListItemView.prototype.templates,{titleBar:a})}();var j=g.extend({className:g.prototype.className+" dataset-collection-element",_swapNewRender:function(a){g.prototype._swapNewRender.call(this,a);var b=this.model.get("state")||"ok";return this.$el.addClass("state-"+b),this.$el},toString:function(){var a=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+a+")"}});return{DCListItemView:g,DCEListItemView:h,DatasetDCEListItemView:i,NestedDCDCEListItemView:j}});
//# sourceMappingURL=../../../maps/mvc/collection/collection-li.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/collection/list-collection-creator.js b/static/scripts/mvc/collection/list-collection-creator.js
new file mode 100644
index 00000000000..db14a262eee
--- /dev/null
+++ b/static/scripts/mvc/collection/list-collection-creator.js
@@ -0,0 +1,2 @@
+define(["mvc/dataset/states","mvc/ui/error-modal","utils/localization"],function(a,b){function c(b){var c=b.toJSON().filter(function(b){return"dataset"===b.history_content_type&&b.state===a.OK});return c}function d(){b("Use the checkboxes at the left of the dataset names to select them. Selected datasets should be error-free and should have completed running.",f)}function e(a){var b="New Dataset List",e=c(a).map(function(a){return{id:a.id,name:a.name,src:"dataset"===a.history_content_type?"hda":"hdca"}});return e.length?a.createHDCA(e,"list",b):(d(),jQuery.Deferred().reject(f))}var f="No valid datasets were selected";return{validElements:c,noValidElementsMessage:f,noValidElementsErrorModal:d,createListHDCA:e}});
+//# sourceMappingURL=../../../maps/mvc/collection/list-collection-creator.js.map
\ No newline at end of file
diff --git a/static/scripts/mvc/collection/list-of-pairs-collection-creator.js b/static/scripts/mvc/collection/list-of-pairs-collection-creator.js
new file mode 100644
index 00000000000..33f1c0d2907
--- /dev/null
+++ b/static/scripts/mvc/collection/list-of-pairs-collection-creator.js
@@ -0,0 +1,2 @@
+define(["utils/levenshtein","utils/natural-sort","mvc/collection/list-collection-creator","mvc/base-mvc","utils/localization"],function(a,b,c,d,e){function f(a){function b(){return c.length||(c=[new RegExp(this.filters[0]),new RegExp(this.filters[1])]),c}a=a||{},a.createPair=a.createPair||function(a){return this.debug("creating pair:",a.listA[a.indexA].name,a.listB[a.indexB].name),a=a||{},this._pair(a.listA.splice(a.indexA,1)[0],a.listB.splice(a.indexB,1)[0],{silent:!0})};var c=[];return a.preprocessMatch=a.preprocessMatch||function(a){var c=b.call(this);return _.extend(a,{matchTo:a.matchTo.name.replace(c[0],""),possible:a.possible.name.replace(c[1],"")})},function(b){this.debug("autopair _strategy ---------------------------"),b=b||{};var c,d=b.listA,e=b.listB,f=0,g={score:0,index:null},h=[];for(this.debug("starting list lens:",d.length,e.length),this.debug("bestMatch (starting):",JSON.stringify(g,null," "));f
=k?(this.debug("creating pair"),h.push(a.createPair.call(this,{listA:d,indexA:f,listB:e,indexB:g.index})),this.debug("list lens now:",d.length,e.length)):f+=1,!d.length||!e.length)return h}return this.debug("paired:",JSON.stringify(h,null," ")),this.debug("autopair _strategy ---------------------------"),h}}function g(a){var b=c.validElements(a);return b.length?j(b,{historyId:a.historyId}):(c.noValidElementsErrorModal(),jQuery.Deferred().reject(c.noValidElementsMessage))}var h=Backbone.View.extend(d.LoggableMixin).extend({tagName:"li",className:"dataset paired",initialize:function(a){this.pair=a.pair||{}},template:_.template(['<%= pair.forward.name %>','','<%= pair.name %>',"",'<%= pair.reverse.name %>'].join("")),render:function(){return this.$el.attr("draggable",!0).data("pair",this.pair).html(this.template({pair:this.pair})).addClass("flex-column-container"),this},events:{dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_dragstart:function(a){a.currentTarget.style.opacity="0.4",a.originalEvent&&(a=a.originalEvent),a.dataTransfer.effectAllowed="move",a.dataTransfer.setData("text/plain",JSON.stringify(this.pair)),this.$el.parent().trigger("pair.dragstart",[this])},_dragend:function(a){a.currentTarget.style.opacity="1.0",this.$el.parent().trigger("pair.dragend",[this])},_sendToParent:function(a){this.$el.parent().trigger(a)},toString:function(){return"PairView("+this.pair.name+")"}}),i=Backbone.View.extend(d.LoggableMixin).extend({className:"collection-creator flex-row-container",initialize:function(a){this.metric("PairedCollectionCreator.initialize",a),a=_.defaults(a,{datasets:[],filters:this.DEFAULT_FILTERS,automaticallyPair:!0,strategy:"lcs",matchPercentage:.9,twoPassAutopairing:!0}),this.initialList=a.datasets,this.historyId=a.historyId,this.filters=this.commonFilters[a.filters]||this.commonFilters[this.DEFAULT_FILTERS],_.isArray(a.filters)&&(this.filters=a.filters),this.automaticallyPair=a.automaticallyPair,this.strategy=this.strategies[a.strategy]||this.strategies[this.DEFAULT_STRATEGY],_.isFunction(a.strategy)&&(this.strategy=a.strategy),this.matchPercentage=a.matchPercentage,this.twoPassAutopairing=a.twoPassAutopairing,this.removeExtensions=!0,this.oncancel=a.oncancel,this.oncreate=a.oncreate,this.autoscrollDist=a.autoscrollDist||24,this.unpairedPanelHidden=!1,this.pairedPanelHidden=!1,this.$dragging=null,this.blocking=!1,this._setUpBehaviors(),this._dataSetUp()},commonFilters:{illumina:["_1","_2"],Rs:["_R1","_R2"]},DEFAULT_FILTERS:"illumina",strategies:{simple:"autopairSimple",lcs:"autopairLCS",levenshtein:"autopairLevenshtein"},DEFAULT_STRATEGY:"lcs",_dataSetUp:function(){this.paired=[],this.unpaired=[],this.selectedIds=[],this._sortInitialList(),this._ensureIds(),this.unpaired=this.initialList.slice(0),this.automaticallyPair&&(this.autoPair(),this.once("rendered:initial",function(){this.trigger("autopair")}))},_sortInitialList:function(){this._sortDatasetList(this.initialList)},_sortDatasetList:function(a){return a.sort(function(a,c){return b(a.name,c.name)}),a},_ensureIds:function(){return this.initialList.forEach(function(a){a.hasOwnProperty("id")||(a.id=_.uniqueId())}),this.initialList},_splitByFilters:function(){function a(a,b){return b.test(a.name)}var b=this.filters.map(function(a){return new RegExp(a)}),c=[[],[]];return this.unpaired.forEach(function(d){b.forEach(function(b,e){a(d,b)&&c[e].push(d)})}),c},_addToUnpaired:function(a){var c=function(d,e){if(d===e)return d;var f=Math.floor((e-d)/2)+d,g=b(a.name,this.unpaired[f].name);if(0>g)return c(d,f);if(g>0)return c(f+1,e);for(;this.unpaired[f]&&this.unpaired[f].name===a.name;)f++;return f}.bind(this);this.unpaired.splice(c(0,this.unpaired.length),0,a)},autoPair:function(a){var b=this._splitByFilters(),c=[];return this.twoPassAutopairing&&(c=this.autopairSimple({listA:b[0],listB:b[1]}),b=this._splitByFilters()),a=a||this.strategy,b=this._splitByFilters(),c=c.concat(this[a].call(this,{listA:b[0],listB:b[1]}))},autopairSimple:f({scoreThreshold:function(){return 1},match:function(a){return a=a||{},a.matchTo===a.possible?{index:a.index,score:1}:a.bestMatch}}),autopairLevenshtein:f({scoreThreshold:function(){return this.matchPercentage},match:function(b){b=b||{};var c=a(b.matchTo,b.possible),d=1-c/Math.max(b.matchTo.length,b.possible.length);return d>b.bestMatch.score?{index:b.index,score:d}:b.bestMatch}}),autopairLCS:f({scoreThreshold:function(){return this.matchPercentage},match:function(a){a=a||{};var b=this._naiveStartingAndEndingLCS(a.matchTo,a.possible).length,c=b/Math.max(a.matchTo.length,a.possible.length);return c>a.bestMatch.score?{index:a.index,score:c}:a.bestMatch}}),_naiveStartingAndEndingLCS:function(a,b){for(var c="",d="",e=0,f=0;e=0&&f>=0&&a[e]===b[f];)d=[a[e],d].join(""),e-=1,f-=1;return c+d},_pair:function(a,b,c){c=c||{};var d=this._createPair(a,b,c.name);return this.paired.push(d),this.unpaired=_.without(this.unpaired,a,b),c.silent||this.trigger("pair:new",d),d},_createPair:function(a,b,c){if(!a||!b||a===b)throw new Error("Bad pairing: "+[JSON.stringify(a),JSON.stringify(b)]);return c=c||this._guessNameForPair(a,b),{forward:a,name:c,reverse:b}},_guessNameForPair:function(a,b,c){c=void 0!==c?c:this.removeExtensions;var d=a.name,e=b.name,f=this._naiveStartingAndEndingLCS(d.replace(this.filters[0],""),e.replace(this.filters[1],""));if(c){var g=f.lastIndexOf(".");if(g>0){var h=f.slice(g,f.length);f=f.replace(h,""),d=d.replace(h,""),e=e.replace(h,"")}}return f||d+" & "+e},_unpair:function(a,b){if(b=b||{},!a)throw new Error("Bad pair: "+JSON.stringify(a));return this.paired=_.without(this.paired,a),this._addToUnpaired(a.forward),this._addToUnpaired(a.reverse),b.silent||this.trigger("pair:unpair",[a]),a},unpairAll:function(){for(var a=[];this.paired.length;)a.push(this._unpair(this.paired[0],{silent:!0}));this.trigger("pair:unpair",a)},_pairToJSON:function(a,b){return b=b||"hda",{collection_type:"paired",src:"new_collection",name:a.name,element_identifiers:[{name:"forward",id:a.forward.id,src:b},{name:"reverse",id:a.reverse.id,src:b}]}},createList:function(a){var b=this,c="/api/histories/"+this.historyId+"/contents/dataset_collections",d={type:"dataset_collection",collection_type:"list:paired",name:_.escape(a||b.$(".collection-name").val()),element_identifiers:b.paired.map(function(a){return b._pairToJSON(a)})};return b.blocking=!0,jQuery.ajax(c,{type:"POST",contentType:"application/json",dataType:"json",data:JSON.stringify(d)}).always(function(){b.blocking=!1}).fail(function(a,c,d){b._ajaxErrHandler(a,c,d)}).done(function(a,c,d){b.trigger("collection:created",a,c,d),b.metric("collection:created",a),"function"==typeof b.oncreate&&b.oncreate.call(this,a,c,d)})},_ajaxErrHandler:function(a,b,c){this.error(a,b,c);var d=e("An error occurred while creating this collection");a&&(d+=0===a.readyState&&0===a.status?": "+e("Galaxy could not be reached and may be updating.")+e(" Try again in a few minutes."):a.responseJSON?"
"+JSON.stringify(a.responseJSON)+"
":": "+c),creator._showAlert(d,"alert-danger")},render:function(a){return this.$el.empty().html(i.templates.main()),this._renderHeader(a),this._renderMiddle(a),this._renderFooter(a),this._addPluginComponents(),this.trigger("rendered",this),this},_renderHeader:function(){var a=this.$(".header").empty().html(i.templates.header()).find(".help-content").prepend($(i.templates.helpContent()));return this._renderFilters(),a},_renderFilters:function(){return this.$(".forward-column .column-header input").val(this.filters[0]).add(this.$(".reverse-column .column-header input").val(this.filters[1]))},_renderMiddle:function(){var a=this.$(".middle").empty().html(i.templates.middle());return this.unpairedPanelHidden?this.$(".unpaired-columns").hide():this.pairedPanelHidden&&this.$(".paired-columns").hide(),this._renderUnpaired(),this._renderPaired(),a},_renderUnpaired:function(){var a,b,c=this,d=[],f=this._splitByFilters();return this.$(".forward-column .title").text([f[0].length,e("unpaired forward")].join(" ")),this.$(".forward-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-f[0].length)),this.$(".reverse-column .title").text([f[1].length,e("unpaired reverse")].join(" ")),this.$(".reverse-column .unpaired-info").text(this._renderUnpairedDisplayStr(this.unpaired.length-f[1].length)),this.$(".unpaired-columns .column-datasets").empty(),this.$(".autopair-link").toggle(0!==this.unpaired.length),0===this.unpaired.length?void this._renderUnpairedEmpty():(b=f[1].map(function(a,b){return void 0!==f[0][b]&&f[0][b]!==a&&d.push(c._renderPairButton()),c._renderUnpairedDataset(a)}),a=f[0].map(function(a){return c._renderUnpairedDataset(a)}),a.length||b.length?(this.$(".unpaired-columns .forward-column .column-datasets").append(a).add(this.$(".unpaired-columns .paired-column .column-datasets").append(d)).add(this.$(".unpaired-columns .reverse-column .column-datasets").append(b)),void this._adjUnpairedOnScrollbar()):void this._renderUnpairedNotShown())},_renderUnpairedDisplayStr:function(a){return["(",a," ",e("filtered out"),")"].join("")},_renderUnpairedDataset:function(a){return $("").attr("id","dataset-"+a.id).addClass("dataset unpaired").attr("draggable",!0).addClass(a.selected?"selected":"").append($("").addClass("dataset-name").text(a.name)).data("dataset",a)},_renderPairButton:function(){return $("").addClass("dataset unpaired").append($("").addClass("dataset-name").text(e("Pair these datasets")))},_renderUnpairedEmpty:function(){var a=$('').text("("+e("no remaining unpaired datasets")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(a),a},_renderUnpairedNotShown:function(){var a=$('').text("("+e("no datasets were found matching the current filters")+")");return this.$(".unpaired-columns .paired-column .column-datasets").empty().prepend(a),a},_adjUnpairedOnScrollbar:function(){var a=this.$(".unpaired-columns").last(),b=this.$(".unpaired-columns .reverse-column .dataset").first();if(b.size()){var c=a.offset().left+a.outerWidth(),d=b.offset().left+b.outerWidth(),e=Math.floor(c)-Math.floor(d);this.$(".unpaired-columns .forward-column").css("margin-left",e>0?e:0)}},_renderPaired:function(){if(this.$(".paired-column-title .title").text([this.paired.length,e("paired")].join(" ")),this.$(".unpair-all-link").toggle(0!==this.paired.length),0===this.paired.length)return void this._renderPairedEmpty();this.$(".remove-extensions-link").show(),this.$(".paired-columns .column-datasets").empty();var a=this;this.paired.forEach(function(b){var c=new h({pair:b});a.$(".paired-columns .column-datasets").append(c.render().$el).append(['"].join(""))})},_renderPairedEmpty:function(){var a=$('').text("("+e("no paired datasets yet")+")");return this.$(".paired-columns .column-datasets").empty().prepend(a),a},_renderFooter:function(){var a=this.$(".footer").empty().html(i.templates.footer());return this.$(".remove-extensions").prop("checked",this.removeExtensions),"function"==typeof this.oncancel&&this.$(".cancel-create.btn").show(),a},_addPluginComponents:function(){this._chooseFiltersPopover(".choose-filters-link"),this.$(".help-content i").hoverhighlight(".collection-creator","rgba( 64, 255, 255, 1.0 )")},_chooseFiltersPopover:function(a){function b(a,b){return['"].join("")}var c=$(_.template(['','
',e("Choose from the following filters to change which unpaired reads are shown in the display"),":
",_.values(this.commonFilters).map(function(a){return b(a[0],a[1])}).join(""),"