allow fixing for gateways before Triangle runs from a input file

FESOM2_Mesh_Generation_{{cookiecutter.mesh_name}}/run_all.py

@@ -5,6 +5,8 @@ Bootstrap script to create a new mesh based on the CORE 2 Resolution.
 
 Dr. Paul Gierz, Jan 2020
 """
+import cdo
+import yaml
 
 import os
 import shutil
@@ -18,6 +20,33 @@ if __name__ == "__main__":
     if not os.path.exists("./raw_input_data"):
         os.makedirs("./raw_input_data")
     shutil.copyfile("{{cookiecutter.input_fpath}}", "./raw_input_data/{{cookiecutter.input_fname}}")
+    shutil.copyfile("{{cookiecutter.input_fpath}}", "./raw_input_data/{{cookiecutter.input_fname}}_backup")
+    if os.path.exists("fixup_gateways.yaml"):
+        with open("fixup_gateways.yaml", "r") as gateway_fixes_file:
+            gateway_fixes = yaml.load(gateway_fixes_file)
+    if gateway_fixes:
+        CDO = cdo.Cdo()
+        print("Fixup input data:")
+        for gateway_name, fix_list in gateway_fixes.items():
+            print(gateway_name)
+            print(fix_list)
+            for fix_number, fix in enumerate(fix_list):
+                print(f"* {fix_number}:")
+                fix = [int(item) for item in fix.split(",")]
+                x1 = fix[0]
+                x2 = fix[1]
+                y1 = fix[2]
+                y2 = fix[3]
+                value = fix[4]
+                print("* Setting:")
+                # FIXME:
+                print(f"{y2} ------ {x2}")
+                print(f" |            |")
+                print(f" |    {value} |")
+                print(f" |            |")
+                print(f"{x1} ------ {y1}")
+                output = CDO.setcindexbox(f"{value},{x1},{x2},{y1},{y2}", input="./raw_input_data/{{cookiecutter.input_fname}}")
+                os.rename(output, "./raw_input_data/{{cookiecutter.input_fname}}")
     print(40*"- ")
     print("* MATLAB Part:")
     os.system("matlab.sh -s -S\"--mem=36000\" -M\"-nodisplay -r run('mg_topo_prep_triangle_input.m')\"")