Fix a bug introduced in #5ae04d2955fa (#787)

It broke the use of

reflection_file_reader.any_reflection_file(hklfn+'=hklf+ins/res')

This feature had no test and it did therefore went unnoticed.

iotbx/reflection_file_reader.py

@@ -306,7 +306,7 @@ def as_miller_arrays(self,
           raise Sorry("Can't open files %s.ins or %s.res"
                       "required by the option hklf+ins/res" % ((name,)*2))
         crystal_symmetry = crystal_symmetry_from_ins.extract_from(
-          file=shelx_file)
+          file=shelx_file, close_file=False)
         shelx_file.seek(0)
         remaining = shelx_file.read()
         shelx_file.close()

iotbx/regression/tst_reflection_file_utils.py

@@ -673,6 +673,51 @@ def exercise_get_experimental_phases():
 """
   else: raise Exception_expected
 
+def exercise_hklf_plus_ins_or_res():
+  import textwrap
+  from os import path
+  import shutil
+  from libtbx.test_utils import approx_equal
+
+  try:
+    hklf4 = ['   1   0   0    1.11    0.11',
+             '   0   1  -1    2.22    0.22',
+             '  -1   0   1    4.44    0.44']
+    hklf4 = [li + '\n' for li in hklf4]
+    ins = textwrap.dedent(
+    """\
+    TITL 03srv209 in Pbca
+    CELL 0.71073 7.35 9.541 12.842 90 90 90
+    ZERR 4 0.002 0.002 0.003 0 0 0
+    LATT 1
+    SYMM 0.5-X,-Y,0.5+Z
+    SYMM -X,0.5+Y,0.5-Z
+    SYMM 0.5+X,0.5-Y,-Z
+    SFAC C H O N
+    UNIT 32 40 16 8
+    HKLF 4
+    """)
+    folder = 'temp_data_hklf_plus_ins_res'
+    if not path.exists(folder):
+      os.mkdir(folder)
+    insfn = path.join(folder, '03srv209.ins')
+    hklfn = path.join(folder, '03srv209.hkl')
+    with open(insfn, 'w') as f:
+      f.write(ins)
+    with open(hklfn, 'w') as f:
+      f.writelines(hklf4)
+    rf = reflection_file_reader.any_reflection_file(hklfn+'=hklf+ins/res')
+    ma = rf.as_miller_arrays()[0]
+    cs = ma.crystal_symmetry()
+    assert cs.is_identical_symmetry(
+      crystal.symmetry(unit_cell='7.35 9.541 12.842 90 90 90',
+                       space_group_symbol='Pbca'))
+    assert all(ma.indices() == flex.miller_index([(1,0,0), (0,1,-1), (-1,0,1)]))
+    assert approx_equal(ma.data(), [1.11, 2.22, 4.44])
+    assert approx_equal(ma.sigmas(), [0.11, 0.22, 0.44])
+  finally:
+    shutil.rmtree(folder, ignore_errors=True)
+
 def exercise_extract_miller_array_from_file():
   from iotbx import reflection_file_utils as rfu
   from libtbx.test_utils import approx_equal
@@ -828,6 +873,7 @@ def exercise():
   if (mtz is None):
     print("Skipping iotbx/tst_reflection_file_utils.py: ccp4io not available")
     return
+  exercise_hklf_plus_ins_or_res()
   exercise_get_amplitudes_and_get_phases_deg()
   exercise_get_xtal_data()
   exercise_get_r_free_flags()

iotbx/shelx/crystal_symmetry_from_ins.py

@@ -1,10 +1,12 @@
 from __future__ import absolute_import, division, print_function
 from iotbx import shelx, builders
 
-def extract_from(file_name=None, file=None, max_characters=100000):
+def extract_from(file_name=None, file=None, max_characters=100000,
+                 close_file=True):
   # XXX backward compatibility 2009-09-17 - keep max_characters keyword
   assert [file_name, file].count(None) == 1
-  stream = shelx.command_stream(file=file, filename=file_name)
+  stream = shelx.command_stream(file=file, filename=file_name,
+                                close_when_deleted=close_file)
   parser = shelx.crystal_symmetry_parser(
     stream, builder=builders.crystal_symmetry_builder())
   parser.parse()

iotbx/shelx/lexer.py

@@ -26,14 +26,16 @@ class command_stream(object):
   shelx_commands.update(commands_allowing_atom_names)
 
 
-  def __init__(self, file=None, filename=None):
+  def __init__(self, file=None, filename=None, close_when_deleted=True):
     assert [file, filename].count(None) == 1
     if file is None: file = open(filename)
     self.file = file
+    self.close_when_deleted = close_when_deleted
 
   def __del__(self):
-    if hasattr(self,'file') and hasattr(self.file,'close'):
-      self.file.close()
+    if self.close_when_deleted:
+      if hasattr(self,'file') and hasattr(self.file,'close'):
+        self.file.close()
 
   _cmd_pat = re.compile(r"""
     ^