# Extract Forcings (case.process_forcings)

The final part of the CrocoDash workflow is extracting and processing all the forcing data your simulation needs. This includes initial conditions, boundary conditions, tidal forcings, biogeochemistry data, and more. You process all of this data through the `case.process_forcings` call. `case.process_forcings` wraps a submodule of CrocoDash called extract_forcings. Extract_forcings is a set of scripts to process each forcing, like initial/boundary conditions, tides, etc... extract_forcings also holds a subdirectory called case_setup. This has a driver and config file. This holds all of the specific case information to run the processing scripts. When you run the workflow, this case_setup folder gets copied into your input directory. `case.process_forcings` goes into this subfolder and runs the driver. You can also run the driver yourself through the command-line.

## Workflow Overview

When you run the CrocoDash workflow, configure_forcings and process_forcings:
1. copies a ready-to-run forcing extraction system into your case directories (from `case.configure_forcings`)
2. Runs it to download data from external sources
3. Regrids data to your custom domain
4. Formats everything for MOM6

The key insight: **you don't have to run this from a Jupyter notebook**. You get a complete, standalone extraction system that you can submit to your supercomputer's job queue.

## Directory Structure

When CrocoDash sets up your case, it creates an `extract_forcings` directory in your input folder:

```
input_directory/
├── extract_forcings/
│   ├── driver.py              # Main script that orchestrates everything
│   ├── config.json            # Your case-specific configuration
└── ocnice/                    # Output goes here
    ├── initial_conditions.nc
    ├── boundary_conditions/
    ├── tides/
    └── ...
```


## Command-Line Options

The driver script accepts several options for fine-grained control:

```bash
# Run all forcing extractions
python driver.py --all

# Run only specific forcings
python driver.py --tides
python driver.py --runoff
python driver.py --bgc

# Run multiple forcings
python driver.py --tides --runoff --bgc

# Run all except certain forcings
python driver.py --all --skip bgcic
python driver.py --all --skip conditions bgcic

# Skip entire processing phases
python driver.py --all --skip conditions
```

This flexibility is intentional—you might want to:
- Test individual components without running everything
- Re-run one forcing type if your source data changed
- Run on a supercomputer queue while iterating elsewhere
- Resume after an interrupted run

## The Processing Pipeline

Here's what happens internally when the driver runs:

```
1. Load config.json with your case specifications
   ↓
2. Calls an extract_forcing script
   ↓
3. Outputs all the data to ocnice
```

## Design Philosophy

CrocoDash deliberately **doesn't do all the processing itself**. Instead, it leverages packages:

| Task | Tool | Used By |
|------|------|---------|
| Regridding & OBC extraction | [regional-mom6](https://github.com/COSIMA/regional-mom6) | `regrid_dataset_piecewise.py` & Various Modules |
| Minor processing (fill, mapping, Chlorophyll) | [mom6_bathy](https://github.com/NCAR/mom6_bathy) | Various modules |
| Data formatting | `netCDF4`, `xarray` | Throughout |

If you want to modify how regridding or initial/boundary conditions are processed, the main place to look is `CrocoDash.extract_forcings.regrid_dataset_piecewise`, which calls `regional-mom6` under the hood. You can look at [regional_mom6 documentation](https://regional-mom6.readthedocs.io/en/latest/index.html) for more information, allthrough it may be difficult to tease out how we use regional_mom6 without looking into the code a bit more.

## Example: Running Forcings on Your HPC System

Here's a typical workflow for an HPC system with job queues:

1. **Set up your case locally (or on login node):**
   ```python
   case = Case(...)
   case.configure_forcings(...)  # Sets up all configuration
   ```

3. **Submit extraction as a batch job:**
   ```bash
   cd /path/to/case/input_directory/extract_forcings
   # Activate CrocoDash environment and submit to batch system!
   ```