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Merge pull request #3 from galaxyproject/dev
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Updates to current galaxy dev
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@pcm32
pcm32 committed Jun 1, 2016
2 parents c6da8eb + 25a26d8 commit c0b4119
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Showing 131 changed files with 1,585 additions and 991 deletions.
109 changes: 70 additions & 39 deletions client/galaxy/scripts/layout/scratchbook.js
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Original file line number Diff line number Diff line change
Expand Up @@ -41,45 +41,82 @@ return Backbone.View.extend({
}).on( 'show hide ', function() {
self.buttonLoad.set( { 'toggle': this.visible, 'icon': this.visible && 'fa-eye' || 'fa-eye-slash' } );
});
this.history_cache = {};
},

/** Add a dataset to the frames */
addDataset: function( dataset_id ) {
var self = this;
var current_dataset = null;
if ( Galaxy && Galaxy.currHistoryPanel ) {
var history_id = Galaxy.currHistoryPanel.collection.historyId;
this.history_cache[ history_id ] = { name: Galaxy.currHistoryPanel.model.get( 'name' ), dataset_ids: [] };
Galaxy.currHistoryPanel.collection.each( function( model ) {
!model.get( 'deleted' ) && model.get( 'visible' ) && self.history_cache[ history_id ].dataset_ids.push( model.get( 'id' ) );
});
}
var _findDataset = function( dataset, offset ) {
if ( dataset ) {
var history_details = self.history_cache[ dataset.get( 'history_id' ) ];
if ( history_details && history_details.dataset_ids ) {
var dataset_list = history_details.dataset_ids;
var pos = dataset_list.indexOf( dataset.get( 'id' ) );
if ( pos !== -1 && pos + offset >= 0 && pos + offset < dataset_list.length ) {
return dataset_list[ pos + offset ];
}
}
}
};
var _loadDatasetOffset = function( dataset, offset, frame ) {
var new_dataset_id = _findDataset( dataset, offset );
if ( new_dataset_id ) {
self._loadDataset( new_dataset_id, function( new_dataset, config ) {
current_dataset = new_dataset;
frame.model.set( config );
});
} else {
frame.model.trigger( 'change' );
}
}
this._loadDataset( dataset_id, function( dataset, config ) {
current_dataset = dataset;
self.add( _.extend( { menu: [ { icon : 'fa fa-chevron-circle-left',
tooltip : 'Previous in History',
onclick : function( frame ) { _loadDatasetOffset( current_dataset, -1, frame ) },
disabled : function() { return !_findDataset( current_dataset, -1 ) } },
{ icon : 'fa fa-chevron-circle-right',
tooltip : 'Next in History',
onclick : function( frame ) { _loadDatasetOffset( current_dataset, 1, frame ) },
disabled : function() { return !_findDataset( current_dataset, 1 ) } } ] }, config ) )
});
},

_loadDataset: function( dataset_id, callback ) {
var self = this;
require([ 'mvc/dataset/data' ], function( DATA ) {
var dataset = new DATA.Dataset( { id : dataset_id } );
$.when( dataset.fetch() ).then( function() {
// Construct frame config based on dataset's type.
var frame_config = {
title: dataset.get('name')
},
// HACK: For now, assume 'tabular' and 'interval' are the only
// modules that contain tabular files. This needs to be replaced
// will a is_datatype() function.
is_tabular = _.find( [ 'tabular', 'interval' ] , function( data_type ) {
return dataset.get( 'data_type' ).indexOf( data_type ) !== -1;
});

// Use tabular chunked display if dataset is tabular; otherwise load via URL.
if ( is_tabular ) {
var tabular_dataset = new DATA.TabularDataset( dataset.toJSON() );
_.extend( frame_config, {
content: function( parent_elt ) {
DATA.createTabularDatasetChunkedView({
model : tabular_dataset,
parent_elt : parent_elt,
embedded : true,
height : '100%'
});
}
});
}
else {
_.extend( frame_config, {
url: Galaxy.root + 'datasets/' + dataset.id + '/display/?preview=True'
});
var is_tabular = _.find( [ 'tabular', 'interval' ] , function( data_type ) {
return dataset.get( 'data_type' ).indexOf( data_type ) !== -1;
});
var title = dataset.get( 'name' );
var history_details = self.history_cache[ dataset.get( 'history_id' ) ];
if ( history_details ) {
title = history_details.name + ': ' + title;
}
self.add( frame_config );
callback( dataset, is_tabular ? {
title : title,
url : null,
content : DATA.createTabularDatasetChunkedView({
model : new DATA.TabularDataset( dataset.toJSON() ),
embedded : true,
height : '100%'
}).$el
} : {
title : title,
url : Galaxy.root + 'datasets/' + dataset_id + '/display/?preview=True',
content : null
} );
});
});
},
Expand Down Expand Up @@ -136,15 +173,9 @@ return Backbone.View.extend({
window.location = options.url;
} else if ( !this.active ) {
var $galaxy_main = $( window.parent.document ).find( '#galaxy_main' );
if ( options.target == 'galaxy_main' || options.target == 'center' ){
if ( $galaxy_main.length === 0 ){
var href = options.url;
if ( href.indexOf( '?' ) == -1 )
href += '?';
else
href += '&';
href += 'use_panels=True';
window.location = href;
if ( options.target == 'galaxy_main' || options.target == 'center' ) {
if ( $galaxy_main.length === 0 ) {
window.location = options.url + ( href.indexOf( '?' ) == -1 ? '?' : '&' ) + 'use_panels=True';
} else {
$galaxy_main.attr( 'src', options.url );
}
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6 changes: 6 additions & 0 deletions client/galaxy/scripts/mvc/history/history-model.js
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Original file line number Diff line number Diff line change
Expand Up @@ -435,6 +435,7 @@ var ControlledFetchMixin = {
_.each( filters, function( v, k ){
if( v === true ){ v = 'True'; }
if( v === false ){ v = 'False'; }
if( v === null ){ v = 'None'; }
filterMap.q.push( k );
filterMap.qv.push( v );
});
Expand Down Expand Up @@ -522,6 +523,11 @@ var HistoryCollection = Backbone.Collection
deleted : false,
purged : false,
};
} else {
defaults.filters = {
// TODO: for bypassing defaults on current API
deleted : null,
};
}
return defaults;
},
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