From a1cf05d2e4b4ccc8a6fafa7aa332e0743af0ac83 Mon Sep 17 00:00:00 2001
From: lily-tomkovic-DWR <lily.tomkovic@water.ca.gov>
Date: Fri, 7 Feb 2025 12:32:21 -0800
Subject: [PATCH] create set_nudging cli command (has original comments still)

---
 bdschism/bdschism/config.py      | 23 +++++++++++++
 bdschism/bdschism/set_nudging.py | 59 +++++++++++++++++++++++++++++---
 2 files changed, 78 insertions(+), 4 deletions(-)
 create mode 100644 bdschism/bdschism/config.py

diff --git a/bdschism/bdschism/config.py b/bdschism/bdschism/config.py
new file mode 100644
index 0000000..c297f0f
--- /dev/null
+++ b/bdschism/bdschism/config.py
@@ -0,0 +1,23 @@
+import os
+import platform
+
+def get_settings(setting):
+    settings = {
+        "os.link_style": "symlink" if platform.system() == "Linux" else "junction"
+    }
+    return settings.get(setting)
+    
+def create_link(symlink, source):
+    link_style = get_settings("os.link_style")
+    
+    # remove symlink before setting
+    if os.path.islink(symlink):
+        os.remove(symlink)
+
+    # set the symlink based on operating system spec
+    if link_style == "symlink":
+        os.symlink(source, symlink)
+    elif link_style == "junction":
+        os.system(f'mklink /J "{symlink}" "{source}"')  # Windows junction link
+    else:
+        raise ValueError(f"Unsupported link style: {link_style}")
diff --git a/bdschism/bdschism/set_nudging.py b/bdschism/bdschism/set_nudging.py
index 8c20b42..ed385fc 100644
--- a/bdschism/bdschism/set_nudging.py
+++ b/bdschism/bdschism/set_nudging.py
@@ -19,6 +19,11 @@
 import struct, argparse, re
 import time 
 
+import schimpy.param as parms
+import config
+
+import os
+
 ################# command line application #####################
 
 def create_arg_parser():
@@ -34,12 +39,36 @@ def create_arg_parser():
     )
     parser.add_argument('--suffix', default=None, required=True,
                         help="the suffix desired for the nudging/gr3 files. Ex: 'obshycom' in SAL_nu_obshycom.nc")
-    parser.add_argument('--workdir', default='.', required=False,
-                        required=False, help='Simulation directory path')
+    parser.add_argument('--workdir', default='.', required=True, 
+                        help='Simulation directory path')
     return parser
 
+def get_nudge_list(workdir):
+    fname = os.path.join(workdir,"param.nml")
+    
+    params = parms.read_params(fname)
+    nc_nudge_list = []
+    nc_dict = {1: 'TEM',
+               2: 'SAL',
+               3: 'GEN',
+               4: 'AGE',
+               5: 'SED',
+               6: 'ECO',
+               7: 'ICM',
+               8: 'COS',
+               9: 'FIB',
+               10: 'TIMOR-NOT-ACTIVE',
+               11: 'FBM'}
+
+    for i in range(1, 12):
+        if params._namelist['OPT'][f'inu_tr({i})']['value'] == 2:
+            nc_nudge_list.append(nc_dict[i])
+
+    return nc_nudge_list
+
 def set_nudging(suffix, workdir='.'):
-    """ This is a utility to set up nudging files based on a naming convention common for BayDeltaSCHISM
+    """ This is a utility to set up nudging files based on a naming convention common for BayDeltaSCHISM. 
+    Assumed this is on Linux or admin-priveleged Windows machine.
     
     Parameters
     ---------
@@ -73,7 +102,29 @@ def set_nudging(suffix, workdir='.'):
     expectation that usually the file names will be as-expected up to the suffix:
     "BLAH_nudge.gr3" -> "BLAH_nudge.gr3"
 
-    """    
+    """   
+    # Current configuration, deprecated, we need to transition to VAR_nudge.gr3 and VAR_nu.nc 
+    var_map = {"SAL":"salinity",
+               "TEM":"temperature"}
+
+    nc_nudge_list = get_nudge_list(workdir)
+
+    for MOD in nc_nudge_list:
+        if MOD in var_map.keys():
+            var_in_gr3 = var_map[MOD]
+        else:
+            var_in_gr3 = MOD
+
+        var_gr3_in = "{var_in_gr3}_nudge_{suffix}.gr3".format(**locals())
+        var_nc_in = "{MOD}_nu_{suffix}.nc".format(**locals())
+
+        var_gr3_out = "{MOD}_nudge.gr3".format(**locals())
+        var_nc_out = "{MOD}_nu.nc".format(**locals())
+
+        print(f"{MOD}: Linked {var_gr3_out} to {var_gr3_in}")
+        config.create_link(os.path.join(workdir,var_gr3_out), var_gr3_in)
+        print(f"{MOD}: Linked {var_nc_out} to {var_nc_in}")
+        config.create_link(os.path.join(workdir,var_nc_out), var_nc_in)
 
 def main():
     parser = create_arg_parser()