Merge pull request #1499 from jedwards4b/err_test_improvement1

improve err by removing rundir files and recopying from sta rest dire…

Remove files from the run directory and replace them from the sta rest directory improving the
scope of the err test.

Test suite: scripts_regression_tests.py, ERR.f09_g16.B1850
Test baseline:
Test namelist changes:
Test status: bit for bit
Fixes #416

User interface changes?:

Code review: @jgfouca

scripts/lib/CIME/SystemTests/err.py

@@ -27,15 +27,15 @@ def run_phase(self):
         else:
             dout_s_root = self._case.get_value("DOUT_S_ROOT")
             rundir = self._case.get_value("RUNDIR")
-            logger.info("staging files from archive %s" % dout_s_root)
-            for item in glob.glob(os.path.join(dout_s_root, "*", "hist", "*base")):
-                # NOTE - this loop doesn't do anything because the
-                # _ers_first_phase has already copied the history files in the
-                # rundir adding the .base suffix before the short term archiver runs.
-                # The pattern matching in the env_archive.xml looks for history 
-                # files that match ".nc$" in the rundir in order to copy them
-                # to the DOUT_S_ROOT location so the files with the .base
-                # suffix are never copied. 
+            case = self._case.get_value("CASE")
+            # First remove restart, history and rpointer files from the run directory
+            for item in glob.iglob(os.path.join(rundir, "%s.*"%case)):
+                if not item.endswith("base"):
+                    os.remove(item)
+            for item in glob.iglob(os.path.join(rundir, "rpointer.*")):
+                os.remove(item)
+            # Then replace them from the restart directory
+            for item in glob.iglob(os.path.join(dout_s_root,"rest","*","*")):
                 shutil.copy(item, rundir)
 
             self._ers_second_phase()