Merge branch 'release_18.05' into dev

lib/galaxy/tools/parameters/dynamic_options.py

@@ -276,7 +276,7 @@ def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.separator = elem.get("separator", ",")
         columns = elem.get("column", None)
-        assert columns is not None, "Required 'columns' attribute missing from filter"
+        assert columns is not None, "Required 'column' attribute missing from filter"
         self.columns = [d_option.column_spec_to_index(column) for column in columns.split(",")]
 
     def filter_options(self, options, trans, other_values):
@@ -305,9 +305,9 @@ def __init__(self, d_option, elem):
         Filter.__init__(self, d_option, elem)
         self.pair_separator = elem.get("pair_separator", ",")
         self.name_val_separator = elem.get("name_val_separator", None)
-        self.columns = elem.get("column", None)
-        assert self.columns is not None, "Required 'columns' attribute missing from filter"
-        self.columns = [int(column) for column in self.columns.split(",")]
+        columns = elem.get("column", None)
+        assert columns is not None, "Required 'column' attribute missing from filter"
+        self.columns = [d_option.column_spec_to_index(column) for column in columns.split(",")]
 
     def filter_options(self, options, trans, other_values):
         attr_names = []
@@ -509,7 +509,8 @@ def load_from_parameter(from_parameter, transform_lines=None):
                     full_path = os.path.join(self.tool_param.tool.app.config.tool_data_path, data_file)
                     if os.path.exists(full_path):
                         self.index_file = data_file
-                        self.file_fields = self.parse_file_fields(open(full_path))
+                        with open(full_path) as fh:
+                            self.file_fields = self.parse_file_fields(fh)
                     else:
                         self.missing_index_file = data_file
             elif dataset_file is not None:
@@ -622,8 +623,10 @@ def get_fields(self, trans, other_values):
                 options = self.parse_file_fields(StringIO(contents))
         elif self.tool_data_table:
             options = self.tool_data_table.get_fields()
-        else:
+        elif self.file_fields:
             options = list(self.file_fields)
+        else:
+            options = []
         for filter in self.filters:
             options = filter.filter_options(options, trans, other_values)
         return options
@@ -658,7 +661,7 @@ def get_field_by_name_for_value(self, field_name, value, trans, other_values):
 
     def get_options(self, trans, other_values):
         rval = []
-        if self.file_fields is not None or self.tool_data_table is not None or self.dataset_ref_name is not None:
+        if self.file_fields is not None or self.tool_data_table is not None or self.dataset_ref_name is not None or self.missing_index_file:
             options = self.get_fields(trans, other_values)
             for fields in options:
                 rval.append((fields[self.columns['name']], fields[self.columns['value']], False))