Fix for missing included files on history export and import.

Notes:

If a history was exported previously, galaxy would just serve the cached version.
In that case, it is better to make some changes to the history for example, by re-running
the last job and then exporting it.

Export of histories that haven't been exported previously should work without problems.

(cherry picked from commit 9ea0fee)

lib/galaxy/tools/imp_exp/__init__.py

@@ -175,6 +175,24 @@ def get_tag_str( tag, value ):
                             raise Exception( "Invalid dataset path: %s" % temp_dataset_file_name )
                         if datasets_usage_counts[ temp_dataset_file_name ] == 1:
                             shutil.move( temp_dataset_file_name, hda.file_name )
+
+                            # Import additional files if present. Histories exported previously might not have this attribute set.
+                            dataset_extra_files_path = ''
+                            try:
+                                dataset_extra_files_path = dataset_attrs[ 'extra_files_path' ]
+                            except KeyError:
+                                pass
+
+                            if dataset_extra_files_path:
+                                try:
+                                    file_list = os.listdir( os.path.join( archive_dir, dataset_extra_files_path ) )
+                                except OSError:
+                                    file_list = []
+
+                                if len( file_list ):
+                                    os.mkdir( hda.extra_files_path )
+                                    for extra_file in file_list:
+                                        shutil.move( os.path.join( archive_dir, dataset_extra_files_path, extra_file ), hda.extra_files_path )
                         else:
                             datasets_usage_counts[ temp_dataset_file_name ] -= 1
                             shutil.copyfile( temp_dataset_file_name, hda.file_name )
@@ -372,6 +390,7 @@ def default( self, obj ):
                         "uuid": ( lambda uuid: str( uuid ) if uuid else None )( obj.dataset.uuid ),
                         "annotation": to_unicode( getattr( obj, 'annotation', '' ) ),
                         "tags": get_item_tag_dict( obj ),
+                        "extra_files_path": obj.extra_files_path
                     }
                     if not obj.visible and not include_hidden:
                         rval['exported'] = False

lib/galaxy/tools/imp_exp/export_history.py

@@ -14,13 +14,13 @@
 from galaxy.util.json import dumps, loads
 
 
-def get_dataset_filename( name, ext ):
+def get_dataset_filename( name, ext, hid ):
     """
     Builds a filename for a dataset using its name an extension.
     """
     valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
     base = ''.join( c in valid_chars and c or '_' for c in name )
-    return base + ".%s" % ext
+    return base + "_%s.%s" % (hid, ext)
 
 
 def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ):
@@ -51,9 +51,28 @@ def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, ou
         for dataset_attrs in datasets_attrs:
             if dataset_attrs['exported']:
                 dataset_file_name = dataset_attrs[ 'file_name' ]  # Full file name.
+                dataset_hid = dataset_attrs[ 'hid']
                 dataset_archive_name = os.path.join( 'datasets',
-                                                     get_dataset_filename( dataset_attrs[ 'name' ], dataset_attrs[ 'extension' ] ) )
+                                                     get_dataset_filename( dataset_attrs[ 'name' ], dataset_attrs[ 'extension' ], dataset_hid ) )
                 history_archive.add( dataset_file_name, arcname=dataset_archive_name )
+
+                # Include additional files for example, files/images included in HTML output.
+                extra_files_path = dataset_attrs[ 'extra_files_path' ]
+                if extra_files_path:
+                    try:
+                        file_list = os.listdir( extra_files_path )
+                    except OSError:
+                        file_list = []
+
+                    if len( file_list ):
+                        dataset_extra_files_path = 'datasets/extra_files_path_%s' % dataset_hid
+                        for fname in file_list:
+                            history_archive.add( os.path.join( extra_files_path, fname ),
+                                                arcname=( os.path.join( dataset_extra_files_path, fname ) ) )
+                        dataset_attrs[ 'extra_files_path' ] = dataset_extra_files_path
+                    else:
+                        dataset_attrs[ 'extra_files_path' ] = ''
+
                 # Update dataset filename to be archive name.
                 dataset_attrs[ 'file_name' ] = dataset_archive_name