fix path issue for ref file in bd_calstis

refstis/functions.py

@@ -997,10 +997,9 @@ def bias_subtract_data(filename, biasfile):
     name, ext = os.path.splitext(name)
     trailerfile = os.path.join(path, name + '_bias_subtract_log.txt')
 
-    #biasfile = make_path_safe(biasfile)
-    biasfile = os.path.relpath(biasfile)
+    biasfile = make_path_safe(biasfile)
 
-    pyfits.setval(filename, 'BIASFILE', value=biasfile)
+    pyfits.setval(filename, 'BIASFILE', ext=0, value=biasfile)
     status = basic2d(filename,
                      dqicorr='perform',
                      blevcorr='perform',
@@ -1034,8 +1033,12 @@ def make_path_safe(filename):
         return filename
 
     path, filename = os.path.split(filename)
+    #-- Calstis wants the '/' at the end
+    if not path.endswith('/'):
+        path += '/'
 
     os.environ['refdir'] = path
+
     filename = 'refdir$'+filename
 
     return filename

refstis/pipeline.py

@@ -877,10 +877,7 @@ def run(config_file='config.yaml'):
             raise KeyError("oref environment must be set to run the pipeline.")
         else:
             os.environ['oref'] = data['oref']
-
-    # -- used when files are too long for calstis to process
-    os.environ[data['tmp_env']] = data['tmp_path']
-
+
     pop_db.main()
 
     all_folders = get_new_periods(data['products_directory'], data)