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110 changes: 92 additions & 18 deletions
110
abr-testing/abr_testing/protocol_simulation/abr_sim_check.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,108 @@ | ||
| """Check ABR Protocols Simulate Successfully.""" | ||
| from abr_testing.protocol_simulation import simulation_metrics | ||
| import os | ||
| import traceback | ||
| from pathlib import Path | ||
| from typing import Dict, List, Tuple, Union | ||
| import traceback | ||
|
|
||
|
|
||
| def run(file_to_simulate: Path) -> None: | ||
| def run( | ||
| file_dict: Dict[str, Dict[str, Union[str, Path]]], labware_defs: List[Path] | ||
| ) -> None: | ||
| """Simulate protocol and raise errors.""" | ||
| protocol_name = file_to_simulate.stem | ||
| try: | ||
| simulation_metrics.main(file_to_simulate, False) | ||
| except Exception: | ||
| print(f"Error in protocol: {protocol_name}") | ||
| traceback.print_exc() | ||
| for file in file_dict: | ||
| path = file_dict[file]["path"] | ||
| csv_params = "" | ||
| try: | ||
| csv_params = str(file_dict[file]["csv"]) | ||
| except KeyError: | ||
| pass | ||
| try: | ||
| print(f"Simulating {file}") | ||
| simulation_metrics.main( | ||
| protocol_file_path=Path(path), | ||
| save=False, | ||
| parameters=csv_params, | ||
| extra_files=labware_defs, | ||
| ) | ||
| except Exception as e: | ||
| traceback.print_exc() | ||
| print(str(e)) | ||
| print("\n") | ||
|
|
||
|
|
||
| def search(seq: str, dictionary: dict) -> str: | ||
| """Search for specific sequence in file.""" | ||
| for key in dictionary.keys(): | ||
| parts = key.split("_") | ||
| if parts[0] == seq: | ||
| return key | ||
| return "" | ||
|
|
||
|
|
||
| def get_files() -> Tuple[Dict[str, Dict[str, Union[str, Path]]], List[Path]]: | ||
| """Map protocols with corresponding csv files.""" | ||
| file_dict: Dict[str, Dict[str, Union[str, Path]]] = {} | ||
| labware_defs = [] | ||
| for root, directories, _ in os.walk(root_dir): | ||
| for directory in directories: | ||
| if directory == "active_protocols": | ||
| active_dir = os.path.join(root, directory) | ||
| for file in os.listdir( | ||
| active_dir | ||
| ): # Iterate over files in `active_protocols` | ||
| if file.endswith(".py") and file not in exclude: | ||
| file_dict[file] = {} | ||
| file_dict[file]["path"] = Path( | ||
| os.path.abspath( | ||
| os.path.join(root_dir, os.path.join(directory, file)) | ||
| ) | ||
| ) | ||
| if directory == "csv_parameters": | ||
| active_dir = os.path.join(root, directory) | ||
| for file in os.listdir( | ||
| active_dir | ||
| ): # Iterate over files in `active_protocols` | ||
| if file.endswith(".csv") and file not in exclude: | ||
| search_str = file.split("_")[0] | ||
| protocol = search(search_str, file_dict) | ||
| if protocol: | ||
| file_dict[protocol]["csv"] = str( | ||
| os.path.abspath( | ||
| os.path.join( | ||
| root_dir, os.path.join(directory, file) | ||
| ) | ||
| ) | ||
| ) | ||
| if directory == "custom_labware": | ||
| active_dir = os.path.join(root, directory) | ||
| for file in os.listdir( | ||
| active_dir | ||
| ): # Iterate over files in `active_protocols` | ||
| if file.endswith(".json") and file not in exclude: | ||
| labware_defs.append( | ||
| Path( | ||
| os.path.abspath( | ||
| os.path.join( | ||
| root_dir, os.path.join(directory, file) | ||
| ) | ||
| ) | ||
| ) | ||
| ) | ||
| return (file_dict, labware_defs) | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| # Directory to search | ||
| global root_dir | ||
| root_dir = "abr_testing/protocols" | ||
|
|
||
| global exclude | ||
| exclude = [ | ||
| "__init__.py", | ||
| "helpers.py", | ||
| "shared_vars_and_funcs.py", | ||
| ] | ||
| # Walk through the root directory and its subdirectories | ||
| for root, dirs, files in os.walk(root_dir): | ||
| for file in files: | ||
| if file.endswith(".py"): # If it's a Python file | ||
| if file in exclude: | ||
| continue | ||
| file_path = Path(os.path.join(root, file)) | ||
| print(f"Simulating protocol: {file_path.stem}") | ||
| run(file_path) | ||
| print("Simulating Protocols") | ||
| file_dict, labware_defs = get_files() | ||
| # print(file_dict) | ||
| run(file_dict, labware_defs) |
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