Fix template

Author: rbeucher

src/access_mopper/examples/batch_config.yml

@@ -22,8 +22,8 @@ grid_label: gn
 activity_id: CMIP
 
 # Required: Input and output paths
-input_folder: /g/data/p73/archive/CMIP7/ACCESS-ESM1-6/spinup/JuneSpinUp-JuneSpinUp-bfaa9c5b
-output_folder: /scratch/tm70/rb5533/mopper_output
+input_folder: "/g/data/p73/archive/CMIP7/ACCESS-ESM1-6/spinup/JuneSpinUp-JuneSpinUp-bfaa9c5b"
+output_folder: "/scratch/tm70/rb5533/mopper_output"
 
 
 # Optional: File patterns for each variable

src/access_mopper/templates/cmor_job_script.j2

@@ -17,29 +17,20 @@ export CMOR_TRACKER_DB="{{ db_path }}"
 export VARIABLE="{{ variable }}"
 
 # Run the CMORisation for this variable
-python -c "
-import os
-import glob
-import sys
+python -c "import os, glob, sys, json
 from pathlib import Path
-
-# Add any necessary paths
 sys.path.insert(0, '{{ package_path }}')
-
 from access_mopper import ACCESS_ESM_CMORiser
 from access_mopper.tracking import TaskTracker
 
-# Configuration
-config = {{ config|tojson }}
+config = json.loads('{{ config | tojson | replace(\"'\", \"\\'\") }}')
 variable = os.environ['VARIABLE']
 db_path = os.environ['CMOR_TRACKER_DB']
 
-# Find input files
 input_folder = config['input_folder']
 pattern = config.get('file_patterns', {}).get(variable)
 if not pattern:
     raise ValueError(f'No pattern found for variable {variable}')
-
 full_pattern = str(Path(input_folder) / pattern)
 input_files = glob.glob(full_pattern)
 if not input_files:
@@ -48,18 +39,14 @@ if not input_files:
 print(f'Processing {variable} with {len(input_files)} files')
 
 try:
-    # Initialize tracking
     exp = config['experiment_id']
     tracker = TaskTracker(Path(db_path))
     tracker.add_task(variable, exp)
-
     if tracker.is_done(variable, exp):
         print(f'Skipped: {variable} (already done)')
         sys.exit(0)
-
     tracker.mark_running(variable, exp)
 
-    # Create CMORiser with Dask parallelization
     cmoriser = ACCESS_ESM_CMORiser(
         input_paths=input_files,
         compound_name=variable,
@@ -71,19 +58,13 @@ try:
         output_path=config['output_folder'],
         drs_root=config.get('drs_root'),
     )
-
-    # Run the CMORisation
     cmoriser.run()
     tracker.mark_done(variable, exp)
-
     print(f'Completed: {variable}')
-
 except Exception as e:
     print(f'Error processing {variable}: {e}', file=sys.stderr)
     try:
-        exp = config['experiment_id']
-        tracker = TaskTracker(Path(db_path))
         tracker.mark_failed(variable, exp, str(e))
     except:
         pass
-    sys.exit(1)
+    sys.exit(1)"