From 0d641759c67e58f3ff35db553dcfa099a27af1b0 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 23 Mar 2023 14:45:45 +0000
Subject: [PATCH 01/11] Added a tool to load area so it is the same everywhere

---
 bgcval2/functions/AirSeaFluxCO2.py |  3 ++-
 bgcval2/functions/BenCa.py         |  3 ++-
 bgcval2/functions/InvtAlk.py       |  3 ++-
 bgcval2/functions/TotalIntPP.py    |  6 ++----
 bgcval2/functions/dust.py          |  3 ++-
 bgcval2/functions/globalVolMean.py |  9 ++++++---
 bgcval2/functions/ice.py           |  5 +++--
 bgcval2/functions/tools.py         | 17 +++++++++++++++++
 8 files changed, 36 insertions(+), 13 deletions(-)
 create mode 100644 bgcval2/functions/tools.py

diff --git a/bgcval2/functions/AirSeaFluxCO2.py b/bgcval2/functions/AirSeaFluxCO2.py
index 93116547..fe4acbef 100644
--- a/bgcval2/functions/AirSeaFluxCO2.py
+++ b/bgcval2/functions/AirSeaFluxCO2.py
@@ -32,6 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
+from tools import load_area
 
 global loaded_area_and_mask
 global tmask
@@ -46,7 +47,7 @@ def load_area_and_mask(areafile):
     if isinstance(areafile, list) and len(areafile)==1:
         areafile = areafile[0]
     nc = dataset(areafile, 'r')
-    area = nc.variables['e2t'][:] * nc.variables['e1t'][:]
+    area = load_area(nc)
     nc.close()
     loaded_area_and_mask = True
     return area
diff --git a/bgcval2/functions/BenCa.py b/bgcval2/functions/BenCa.py
index e62cba89..65c66007 100644
--- a/bgcval2/functions/BenCa.py
+++ b/bgcval2/functions/BenCa.py
@@ -32,6 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
+from tools import load_area
 
 global loaded_area_and_mask
 global tmask
@@ -48,7 +49,7 @@ def load_area_and_mask(areafile):
     else:
         raise ValueError(f"{areafile} must be a length=1 list containing a single file descriptor.")
     nc = dataset(areafile, 'r')
-    area = nc.variables['e2t'][:] * nc.variables['e1t'][:]
+    area = load_area(nc)
     nc.close()
     loaded_area_and_mask = True
     return area
diff --git a/bgcval2/functions/InvtAlk.py b/bgcval2/functions/InvtAlk.py
index 88b7d30e..356a44e3 100644
--- a/bgcval2/functions/InvtAlk.py
+++ b/bgcval2/functions/InvtAlk.py
@@ -32,6 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
+from tools import load_area
 
 global loaded_area_and_mask
 global tmask
@@ -48,7 +49,7 @@ def load_area_and_mask(areafile):
     else:
         raise ValueError(f"{areafile} must be a length=1 list containing a single file descriptor.")
     nc = dataset(areafile, 'r')
-    area = nc.variables['e2t'][:] * nc.variables['e1t'][:]
+    area = load_area(nc)
     nc.close()
     loaded_area_and_mask = True
     return area
diff --git a/bgcval2/functions/TotalIntPP.py b/bgcval2/functions/TotalIntPP.py
index 6226fc56..5b0e0bdf 100644
--- a/bgcval2/functions/TotalIntPP.py
+++ b/bgcval2/functions/TotalIntPP.py
@@ -31,6 +31,7 @@
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
 from bgcval2.functions.standard_functions import find_best_var
+from tools import load_area
 
 global loadedArea
 global model_area
@@ -41,10 +42,7 @@
 
 def loadDataMask(gridfn):
     nc = dataset(gridfn,'r')
-    try:
-        model_area = nc.variables['area'][:]
-    except:
-         model_area = nc.variables['e1t'][:]*nc.variables['e2t'][:]
+    model_area = load_area(nc)
     nc.close()
     loadedArea = True
     return model_area
diff --git a/bgcval2/functions/dust.py b/bgcval2/functions/dust.py
index 702f71f9..02aa64db 100644
--- a/bgcval2/functions/dust.py
+++ b/bgcval2/functions/dust.py
@@ -42,7 +42,8 @@ def loadDataMask(gridfn):
     global loadedArea
     global masked_area
     nc = dataset(gridfn,'r')
-    masked_area = nc.variables['e2t'][:] * nc.variables['e1t'][:]*nc.variables['tmask'][0]
+    area = load_area(nc)
+    masked_area = area *nc.variables['tmask'][0]
     nc.close()
     loadedArea = True
 
diff --git a/bgcval2/functions/globalVolMean.py b/bgcval2/functions/globalVolMean.py
index 5d7f9ebb..86812f36 100644
--- a/bgcval2/functions/globalVolMean.py
+++ b/bgcval2/functions/globalVolMean.py
@@ -31,15 +31,18 @@
 
 import numpy as np
 from bgcval2.functions.standard_functions import choose_best_var 
-
+from tools import load_area
 
 def calc_vol(nc):
     """
     Calculate volume from the (grid-T) netcdf file.
     """
-    area = nc.variables['area'][:]
+    area = load_area(area)
     thkcello = nc.variables['thkcello'][:]
-    area = area[None, None,:, :]
+    if area.ndim == 4:
+        area = area[None, None,:, :]
+    if area.ndim == 3:
+        area = area[None, :, :]
     return thkcello * area
 
 
diff --git a/bgcval2/functions/ice.py b/bgcval2/functions/ice.py
index e719d22b..c74b0735 100644
--- a/bgcval2/functions/ice.py
+++ b/bgcval2/functions/ice.py
@@ -32,6 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
+from tools import load_area
 
 global loaded_area_and_mask
 global tmask
@@ -50,7 +51,7 @@ def load_area_and_mask(gridfn, maskname,):
         gridfn = gridfn[0]
     nc = dataset(gridfn, 'r')
     tmask = nc.variables[maskname][0]
-    area = nc.variables['e2t'][:] * nc.variables['e1t'][:]
+    area = load_area(nc)
     lat = nc.variables['nav_lat'][:]
     nc.close()
     loaded_area_and_mask = True
@@ -74,7 +75,7 @@ def calculate_ice_extent(nc, keys, **kwargs):
     if 'area' not in nc.variables and not loaded_area_and_mask:
         area, tmask, lat = load_area_and_mask(areafile, maskname)
     else:
-        area = nc.variables['area'][:]
+        area = load_area(nc)
         lat = nc.variables['nav_lat'][:]
         tmask = nc.variables[keys[0]][:].squeeze().mask
 
diff --git a/bgcval2/functions/tools.py b/bgcval2/functions/tools.py
new file mode 100644
index 00000000..b7173e82
--- /dev/null
+++ b/bgcval2/functions/tools.py
@@ -0,0 +1,17 @@
+
+
+import numpy as np
+from bgcval2.functions.standard_functions import choose_best_var
+
+
+def load_area(nc):
+    """
+    Generic tool for loading area:
+    """
+    area_keys = ['area', 'area_grid_T', 'area_grid_W', 'area_grid_V', 'area_grid_U']
+    if set(area_keys).intersection(set(nc.variables.keys()): 
+         return choose_best_var(nc, area_keys)
+    else:
+        area = nc.variables['e1t'][:]*nc.variables['e2t'][:]
+
+

From 05c2d6017236c5fc0806dc4d2c1440e918873f0f Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 23 Mar 2023 15:57:29 +0000
Subject: [PATCH 02/11] Working version

---
 bgcval2/download_from_mass.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/bgcval2/download_from_mass.py b/bgcval2/download_from_mass.py
index 461e24c8..cdd8488b 100755
--- a/bgcval2/download_from_mass.py
+++ b/bgcval2/download_from_mass.py
@@ -409,7 +409,9 @@ def download_from_mass(
     outputFold = folder([paths.ModelFolder_pref,  jobID,] )
     # make this folder group writeable. 
     st = os.stat(outputFold)
-    os.chmod(outputFold, st.st_mode | stat.S_IWGRP)
+
+    try: os.chmod(outputFold, st.st_mode | stat.S_IWGRP)
+    except: pass
 
     deleteBadLinksAndZeroSize(outputFold, jobID)
 
@@ -417,7 +419,8 @@ def download_from_mass(
     deleteBadLinksAndZeroSize(outputFold, jobID)
 
     # Set up a file to save command to a new file.
-    download_script_path = ''.join([folder('mass_scripts/'), jobID,'.sh'])
+    username = os.getlogin()
+    download_script_path = ''.join([folder('mass_scripts/'), jobID,'_',username, '.sh'])
     header_lines = ['# Run this script on mass-cli1.jasmin.ac.uk\n',]
     header_lines.append('# from login1.jasmin.ac.uk, ssh to the mass machine:\n#     ssh -X  mass-cli\n')
     header_lines.append(''.join(['# run script with:\n# source ', os.path.abspath(download_script_path),'\n']))
@@ -483,7 +486,8 @@ def download_from_mass(
     if auto_download:
         shared_file_path = os.path.join(paths.shared_mass_scripts, os.path.basename(download_script_path))
         print('writing file in shared path', shared_file_path)
-        shutil.copy(download_script_path, shared_file_path)
+        try: shutil.copy(download_script_path, shared_file_path)
+        except: pass
 
     fixFilePaths(outputFold, jobID, debug=False,)
     deleteBadLinksAndZeroSize(outputFold, jobID, debug=False,)

From fce11db726a37c73de5b0c29877e41e3e21baff5 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 23 Mar 2023 16:06:26 +0000
Subject: [PATCH 03/11] bugfix here.

---
 bgcval2/functions/AirSeaFluxCO2.py |  2 +-
 bgcval2/functions/BenCa.py         |  2 +-
 bgcval2/functions/InvtAlk.py       |  2 +-
 bgcval2/functions/TotalIntPP.py    |  2 +-
 bgcval2/functions/globalVolMean.py |  2 +-
 bgcval2/functions/ice.py           |  2 +-
 bgcval2/functions/tools.py         | 40 +++++++++++++++++++++++++++---
 7 files changed, 42 insertions(+), 10 deletions(-)

diff --git a/bgcval2/functions/AirSeaFluxCO2.py b/bgcval2/functions/AirSeaFluxCO2.py
index fe4acbef..b320435d 100644
--- a/bgcval2/functions/AirSeaFluxCO2.py
+++ b/bgcval2/functions/AirSeaFluxCO2.py
@@ -32,7 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
-from tools import load_area
+from bgcval2.functions.tools import load_area
 
 global loaded_area_and_mask
 global tmask
diff --git a/bgcval2/functions/BenCa.py b/bgcval2/functions/BenCa.py
index 65c66007..40ea0d18 100644
--- a/bgcval2/functions/BenCa.py
+++ b/bgcval2/functions/BenCa.py
@@ -32,7 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
-from tools import load_area
+from bgcval2.functions.tools import load_area
 
 global loaded_area_and_mask
 global tmask
diff --git a/bgcval2/functions/InvtAlk.py b/bgcval2/functions/InvtAlk.py
index 356a44e3..dc8d05f3 100644
--- a/bgcval2/functions/InvtAlk.py
+++ b/bgcval2/functions/InvtAlk.py
@@ -32,7 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
-from tools import load_area
+from bgcval2.functions.tools import load_area
 
 global loaded_area_and_mask
 global tmask
diff --git a/bgcval2/functions/TotalIntPP.py b/bgcval2/functions/TotalIntPP.py
index 5b0e0bdf..294ee877 100644
--- a/bgcval2/functions/TotalIntPP.py
+++ b/bgcval2/functions/TotalIntPP.py
@@ -31,7 +31,7 @@
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
 from bgcval2.functions.standard_functions import find_best_var
-from tools import load_area
+from bgcval2.functions.tools import load_area
 
 global loadedArea
 global model_area
diff --git a/bgcval2/functions/globalVolMean.py b/bgcval2/functions/globalVolMean.py
index 86812f36..5130e5f5 100644
--- a/bgcval2/functions/globalVolMean.py
+++ b/bgcval2/functions/globalVolMean.py
@@ -31,7 +31,7 @@
 
 import numpy as np
 from bgcval2.functions.standard_functions import choose_best_var 
-from tools import load_area
+from bgcval2.functions.tools import load_area
 
 def calc_vol(nc):
     """
diff --git a/bgcval2/functions/ice.py b/bgcval2/functions/ice.py
index c74b0735..0b830584 100644
--- a/bgcval2/functions/ice.py
+++ b/bgcval2/functions/ice.py
@@ -32,7 +32,7 @@
 import numpy as np
 from bgcval2.bgcvaltools.dataset import dataset
 from bgcval2.functions.get_kwarg_file import get_kwarg_file
-from tools import load_area
+from bgcval2.functions.tools import load_area
 
 global loaded_area_and_mask
 global tmask
diff --git a/bgcval2/functions/tools.py b/bgcval2/functions/tools.py
index b7173e82..c92d69b2 100644
--- a/bgcval2/functions/tools.py
+++ b/bgcval2/functions/tools.py
@@ -1,3 +1,33 @@
+# Copyright 2023, Plymouth Marine Laboratory
+#
+# This file is part of the bgc-val library.
+#
+# bgc-val is free software: you can redistribute it and/or modify it
+# under the terms of the Revised Berkeley Software Distribution (BSD) 3-clause license.
+
+# bgc-val is distributed in the hope that it will be useful, but
+# without any warranty; without even the implied warranty of merchantability
+# or fitness for a particular purpose. See the revised BSD license for more details.
+# You should have received a copy of the revised BSD license along with bgc-val.
+# If not, see <http://opensource.org/licenses/BSD-3-Clause>.
+#
+# Address:
+# Plymouth Marine Laboratory
+# Prospect Place, The Hoe
+# Plymouth, PL1 3DH, UK
+#
+# Email:
+# ledm@pml.ac.uk
+#
+"""
+.. module:: tools
+   :platform: Unix
+   :synopsis: This uses some tools for the functions library.
+
+.. moduleauthor:: Lee de Mora <ledm@pml.ac.uk>
+
+"""
+
 
 
 import numpy as np
@@ -9,9 +39,11 @@ def load_area(nc):
     Generic tool for loading area:
     """
     area_keys = ['area', 'area_grid_T', 'area_grid_W', 'area_grid_V', 'area_grid_U']
-    if set(area_keys).intersection(set(nc.variables.keys()): 
-         return choose_best_var(nc, area_keys)
-    else:
+    if set(area_keys).intersection(set(nc.variables.keys())): 
+        area = choose_best_var(nc, area_keys)
+    elif set(['e1t', 'e2t']).intersection(set(nc.variables.keys())):
         area = nc.variables['e1t'][:]*nc.variables['e2t'][:]
-
+    else:
+        raise ValueError('Unable to load or calculate area from this file.')
+    return area
 

From 544e45f6fcac17fff8ca3126c1dfdf36cef0b378 Mon Sep 17 00:00:00 2001
From: Valeriu Predoi <valeriu.predoi@gmail.com>
Date: Thu, 23 Mar 2023 16:48:37 +0000
Subject: [PATCH 04/11] fix how code gets user name for portability

---
 bgcval2/download_from_mass.py | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/bgcval2/download_from_mass.py b/bgcval2/download_from_mass.py
index cdd8488b..e79804ab 100755
--- a/bgcval2/download_from_mass.py
+++ b/bgcval2/download_from_mass.py
@@ -419,7 +419,11 @@ def download_from_mass(
     deleteBadLinksAndZeroSize(outputFold, jobID)
 
     # Set up a file to save command to a new file.
-    username = os.getlogin()
+    try:
+        username = os.getlogin()
+    except OSError:
+        import getpass
+        username = getpass.getuser()
     download_script_path = ''.join([folder('mass_scripts/'), jobID,'_',username, '.sh'])
     header_lines = ['# Run this script on mass-cli1.jasmin.ac.uk\n',]
     header_lines.append('# from login1.jasmin.ac.uk, ssh to the mass machine:\n#     ssh -X  mass-cli\n')

From 5d42c9474e7da7823cafe88a6f0246bd854894a2 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 23 Mar 2023 17:13:22 +0000
Subject: [PATCH 05/11] bugfix

---
 bgcval2/functions/globalVolMean.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bgcval2/functions/globalVolMean.py b/bgcval2/functions/globalVolMean.py
index 5130e5f5..e9b2bb43 100644
--- a/bgcval2/functions/globalVolMean.py
+++ b/bgcval2/functions/globalVolMean.py
@@ -37,7 +37,7 @@ def calc_vol(nc):
     """
     Calculate volume from the (grid-T) netcdf file.
     """
-    area = load_area(area)
+    area = load_area(nc)
     thkcello = nc.variables['thkcello'][:]
     if area.ndim == 4:
         area = area[None, None,:, :]

From 4e73a34af1771fdf0b4f47cbfdf1330675036722 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 23 Mar 2023 17:20:33 +0000
Subject: [PATCH 06/11] Update bgcval2/download_from_mass.py

Co-authored-by: Valeriu Predoi <valeriu.predoi@gmail.com>
---
 bgcval2/download_from_mass.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bgcval2/download_from_mass.py b/bgcval2/download_from_mass.py
index e79804ab..b5d41a94 100755
--- a/bgcval2/download_from_mass.py
+++ b/bgcval2/download_from_mass.py
@@ -411,7 +411,8 @@ def download_from_mass(
     st = os.stat(outputFold)
 
     try: os.chmod(outputFold, st.st_mode | stat.S_IWGRP)
-    except: pass
+    except OSError:
+        pass
 
     deleteBadLinksAndZeroSize(outputFold, jobID)
 

From 7a80b9a02f7e929b9b64ffa1e6135b791d4b5d70 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 23 Mar 2023 17:20:51 +0000
Subject: [PATCH 07/11] Update bgcval2/functions/tools.py

Co-authored-by: Valeriu Predoi <valeriu.predoi@gmail.com>
---
 bgcval2/functions/tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bgcval2/functions/tools.py b/bgcval2/functions/tools.py
index c92d69b2..142081b7 100644
--- a/bgcval2/functions/tools.py
+++ b/bgcval2/functions/tools.py
@@ -44,6 +44,6 @@ def load_area(nc):
     elif set(['e1t', 'e2t']).intersection(set(nc.variables.keys())):
         area = nc.variables['e1t'][:]*nc.variables['e2t'][:]
     else:
-        raise ValueError('Unable to load or calculate area from this file.')
+        raise ValueError(f"Provided {nc} file doesn't contain any of permitted area variables {area_keys}")        
     return area
 

From b98cb269f4afac96a8359c7ce2a13ed8d6458586 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 23 Mar 2023 17:21:01 +0000
Subject: [PATCH 08/11] Update bgcval2/download_from_mass.py

---
 bgcval2/download_from_mass.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bgcval2/download_from_mass.py b/bgcval2/download_from_mass.py
index b5d41a94..e91881e3 100755
--- a/bgcval2/download_from_mass.py
+++ b/bgcval2/download_from_mass.py
@@ -425,7 +425,7 @@ def download_from_mass(
     except OSError:
         import getpass
         username = getpass.getuser()
-    download_script_path = ''.join([folder('mass_scripts/'), jobID,'_',username, '.sh'])
+    download_script_path = ''.join([folder('mass_scripts/'), jobID, '_', username, '.sh'])
     header_lines = ['# Run this script on mass-cli1.jasmin.ac.uk\n',]
     header_lines.append('# from login1.jasmin.ac.uk, ssh to the mass machine:\n#     ssh -X  mass-cli\n')
     header_lines.append(''.join(['# run script with:\n# source ', os.path.abspath(download_script_path),'\n']))

From eaf113465de555a9abb0bf3431b26d500871ff83 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Thu, 23 Mar 2023 17:21:12 +0000
Subject: [PATCH 09/11] Update bgcval2/download_from_mass.py

Co-authored-by: Valeriu Predoi <valeriu.predoi@gmail.com>
---
 bgcval2/download_from_mass.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/bgcval2/download_from_mass.py b/bgcval2/download_from_mass.py
index e91881e3..32819f4e 100755
--- a/bgcval2/download_from_mass.py
+++ b/bgcval2/download_from_mass.py
@@ -410,7 +410,8 @@ def download_from_mass(
     # make this folder group writeable. 
     st = os.stat(outputFold)
 
-    try: os.chmod(outputFold, st.st_mode | stat.S_IWGRP)
+    try:
+        os.chmod(outputFold, st.st_mode | stat.S_IWGRP)
     except OSError:
         pass
 

From faefa20e691e2c77626e48b298bf7a6a0c7c46c2 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Mon, 3 Apr 2023 16:15:37 +0100
Subject: [PATCH 10/11] Update bgcval2/functions/tools.py

---
 bgcval2/functions/tools.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/bgcval2/functions/tools.py b/bgcval2/functions/tools.py
index 142081b7..74937784 100644
--- a/bgcval2/functions/tools.py
+++ b/bgcval2/functions/tools.py
@@ -29,7 +29,6 @@
 """
 
 
-
 import numpy as np
 from bgcval2.functions.standard_functions import choose_best_var
 

From 8f9805af7e162a7e82194bf15b63bae5123487f3 Mon Sep 17 00:00:00 2001
From: Lee de Mora <ledm@pml.ac.uk>
Date: Mon, 3 Apr 2023 16:15:53 +0100
Subject: [PATCH 11/11] Added error handling and output.

---
 bgcval2/download_from_mass.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/bgcval2/download_from_mass.py b/bgcval2/download_from_mass.py
index 32819f4e..17b9f8fe 100755
--- a/bgcval2/download_from_mass.py
+++ b/bgcval2/download_from_mass.py
@@ -413,7 +413,7 @@ def download_from_mass(
     try:
         os.chmod(outputFold, st.st_mode | stat.S_IWGRP)
     except OSError:
-        pass
+        print('Unable to change permissions:', outputFold)
 
     deleteBadLinksAndZeroSize(outputFold, jobID)
 
@@ -492,8 +492,10 @@ def download_from_mass(
     if auto_download:
         shared_file_path = os.path.join(paths.shared_mass_scripts, os.path.basename(download_script_path))
         print('writing file in shared path', shared_file_path)
-        try: shutil.copy(download_script_path, shared_file_path)
-        except: pass
+        try: 
+            shutil.copy(download_script_path, shared_file_path)
+        except EnvironmentError:
+            print('Error copying file', download_script_path, 'to', shared_file_path)
 
     fixFilePaths(outputFold, jobID, debug=False,)
     deleteBadLinksAndZeroSize(outputFold, jobID, debug=False,)