API, histories: correct copy to copy both non-deleted and deleted contents by default, add all_datasets flag to support copying only non-deleted; UI, histories: separate out history copy dialog for use in multi-panel (and later: the options menu), include deleted filter in choices

client/galaxy/scripts/mvc/history/history-model.js

@@ -1,3 +1,4 @@
+
 define([
     "mvc/history/history-contents",
     "utils/utils",
@@ -243,7 +244,7 @@ var History = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend(
      *  @fires copied               passed this history and the response JSON from the copy
      *  @returns {xhr}
      */
-    copy : function( current, name ){
+    copy : function( current, name, allDatasets ){
         current = ( current !== undefined )?( current ):( true );
         if( !this.id ){
             throw new Error( 'You must set the history ID before copying it.' );
@@ -256,8 +257,9 @@ var History = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend(
         if( name ){
             postData.name = name;
         }
-
-        //TODO:?? all datasets?
+        if( !allDatasets ){
+            postData.all_datasets = false;
+        }
 
         var history = this,
             copy = jQuery.post( this.urlRoot, postData );

client/galaxy/scripts/mvc/history/multi-panel.js

@@ -1,79 +1,12 @@
 define([
     "mvc/history/history-model",
     "mvc/history/history-panel-edit",
+    "mvc/history/copy-dialog",
     "mvc/base-mvc",
     "utils/ajax-queue",
     "ui/mode-button",
     "ui/search-input"
-], function( HISTORY_MODEL, HPANEL_EDIT, baseMVC, ajaxQueue ){
-//==============================================================================
-/**  */
-function historyCopyDialog( history, options ){
-    options = options || {};
-    // fall back to un-notifying copy
-    if( !( Galaxy && Galaxy.modal ) ){
-        return history.copy();
-    }
-
-    // maybe better as multiselect dialog?
-    var historyName = history.get( 'name' ),
-        defaultCopyName = "Copy of '" + historyName + "'";
-
-    function validateName( name ){
-        if( !name ){
-            if( !Galaxy.modal.$( '#invalid-title' ).size() ){
-                var $invalidTitle = $( '<p/>' ).attr( 'id', 'invalid-title' )
-                    .css({ color: 'red', 'margin-top': '8px' })
-                    .addClass( 'bg-danger' ).text( _l( 'Please enter a valid history title' ) );
-                Galaxy.modal.$( '.modal-body' ).append( $invalidTitle );
-            }
-            return false;
-        }
-        return name;
-    }
-
-    function copyHistory( name ){
-        var $copyIndicator = $( '<p><span class="fa fa-spinner fa-spin"></span> Copying history...</p>' )
-            .css( 'margin-top', '8px' );
-        Galaxy.modal.$( '.modal-body' ).append( $copyIndicator );
-        history.copy( true, name )
-            //TODO: make this unneccessary with pub-sub error
-            .fail( function(){
-                alert( _l( 'History could not be copied. Please contact a Galaxy administrator' ) );
-            })
-            .always( function(){
-                Galaxy.modal.hide();
-            });
-    }
-    function checkNameAndCopy(){
-        var name = Galaxy.modal.$( '#copy-modal-title' ).val();
-        if( !validateName( name ) ){ return; }
-        copyHistory( name );
-    }
-
-    Galaxy.modal.show( _.extend({
-        title   : _l( 'Copying history' ) + ' "' + historyName + '"',
-        body    : $([
-                '<label for="copy-modal-title">',
-                    _l( 'Enter a title for the copied history' ), ':',
-                '</label><br />',
-                '<input id="copy-modal-title" class="form-control" style="width: 100%" value="',
-                    defaultCopyName, '" />'
-            ].join('')),
-        buttons : {
-            'Cancel' : function(){ Galaxy.modal.hide(); },
-            'Copy'   : checkNameAndCopy
-        }
-    }, options ));
-    $( '#copy-modal-title' ).focus().select();
-    $( '#copy-modal-title' ).on( 'keydown', function( ev ){
-        if( ev.keyCode === 13 ){
-            checkNameAndCopy();
-        }
-    });
-}
-
-
+], function( HISTORY_MODEL, HPANEL_EDIT, historyCopyDialog, baseMVC, ajaxQueue ){
 /* ==============================================================================
 TODO:
     rendering/delayed rendering is a mess

lib/galaxy/webapps/galaxy/api/histories.py

@@ -22,6 +22,7 @@ from galaxy.web.base.controller import ImportsHistoryMixin
 
 from galaxy.managers import histories, citations, users
 
+from galaxy import util
 from galaxy.util import string_as_bool
 from galaxy.util import restore_text
 from galaxy.web import url_for
@@ -286,6 +287,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
         :param  payload: (optional) dictionary structure containing:
             * name:             the new history's name
             * history_id:       the id of the history to copy
+            * all_datasets:     copy deleted hdas/hdcas? 'True' or 'False', defaults to True
             * archive_source:   the url that will generate the archive to import
             * archive_type:     'url' (default)
 
@@ -300,6 +302,8 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
             hist_name = restore_text( payload['name'] )
         copy_this_history_id = payload.get( 'history_id', None )
 
+        all_datasets = util.string_as_bool( payload.get( 'all_datasets', True ) )
+
         if "archive_source" in payload:
             archive_source = payload[ "archive_source" ]
             archive_type = payload.get( "archive_type", "url" )
@@ -312,7 +316,7 @@ class HistoriesController( BaseAPIController, ExportsHistoryMixin, ImportsHistor
             decoded_id = self.decode_id( copy_this_history_id )
             original_history = self.history_manager.get_accessible( decoded_id, trans.user, current_history=trans.history )
             hist_name = hist_name or ( "Copy of '%s'" % original_history.name )
-            new_history = original_history.copy( name=hist_name, target_user=trans.user )
+            new_history = original_history.copy( name=hist_name, target_user=trans.user, all_datasets=all_datasets )
 
         # otherwise, create a new empty history
         else: