DataManager: fix bug where default type was not changed for all arrays

iotbx/data_manager/common.py

@@ -101,7 +101,7 @@ def update_all_defaults(self, data_type):
     array_type = [checked_type]
     self.set_default_miller_array_type(array_type)
     for filename in self.get_miller_array_names():
-      for label in self.get_miller_array_labels(filename):
+      for label in self.get_miller_array_all_labels(filename):
         self.set_miller_array_type(filename, label, array_type)
 
   def get_fmodel_params(self):

iotbx/regression/tst_cli_parser.py

@@ -342,6 +342,45 @@ def run(self):
   except Sorry as s:
     assert 'duplicate user_selected_labels' in str(s)
 
+# -----------------------------------------------------------------------------
+def test_update_all_defaults():
+
+  data_dir = os.path.dirname(os.path.abspath(__file__))
+  model_1yjp = os.path.join(data_dir, 'data', '1yjp.pdb')
+  data_mtz = os.path.join(data_dir, 'data', 'phaser_1.mtz')
+
+  class testProgram(ProgramTemplate):
+
+    datatypes = ['model', 'miller_array', 'phil']
+
+    def validate(self):
+      pass
+
+    def run(self):
+      pass
+
+    def get_results(self):
+      return self.data_manager
+
+  dm = run_program(
+    program_class=testProgram,
+    args=['--quiet', '--overwrite', model_1yjp, data_mtz]
+  )
+  dm.update_all_defaults('neutron')
+  assert 'neutron' in dm.get_model_type(model_1yjp)
+  assert 'x_ray' not in dm.get_model_type(model_1yjp)
+
+  # check that all default types are updated even with label selection
+  dm = run_program(
+    program_class=testProgram,
+    args=['--quiet', '--overwrite', model_1yjp, data_mtz,
+          'user_selected=FWT,PHIFWT']
+  )
+  dm.update_all_defaults('electron')
+  for label in dm.get_miller_array_all_labels(data_mtz):
+    assert 'electron' in dm.get_miller_array_type(data_mtz, label)
+    assert 'x_ray' not in dm.get_miller_array_type(data_mtz, label)
+
 # -----------------------------------------------------------------------------
 def test_json():
   class testProgram(ProgramTemplate):
@@ -634,6 +673,7 @@ def get_results(self):
   test_label_parsing()
   test_model_type_parsing()
   test_user_selected_labels()
+  test_update_all_defaults()
   test_json()
   test_diff_params()
   test_check_current_dir()