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"""Helper methods for validating cli entries."""
from enum import Enum
from pathlib import Path
import typer
from folding_studio.utils.path_helpers import extract_files
class SupportedCustomTemplateFile(str, Enum):
"""Supported custom template file extensions."""
CIF = ".cif"
class SupportedCustomMSAFile(str, Enum):
"""Supported custom msa file extensions."""
STO = ".sto"
A3M = ".a3m"
class SupportedTemplateMaskFile(str, Enum):
"""Supported custom template file extensions."""
JSON = ".json"
def extract_and_validate_custom_templates(
paths: list[Path],
) -> list[Path]:
"""Extract and validate a list of path to use as custom templates.
Before checking the files, if a directory path is in the list, its files are extracted.
Args:
paths (list[Path]): List of paths.
Raises:
typer.BadParameter: If a file is not supported.
Returns:
list[Path]: Extracted and validated custom template files path.
"""
extracted_paths = extract_files(paths)
supported_files = [item.value for item in SupportedCustomTemplateFile]
for path in extracted_paths:
if path.suffix not in supported_files:
raise typer.BadParameter(
f"The file '{path}' is not supported. "
f"Only {supported_files} are supported for custom templates."
)
return extracted_paths
def extract_and_validate_custom_msas(paths: list[Path]) -> list[Path]:
"""Extract and validate a list of path to use as custom msas.
Before checking the files, if a directory path is in the list, its files are extracted.
Args:
paths (list[Path]): List of paths.
Raises:
typer.BadParameter: If a file is not supported.
Returns:
list[Path]: Extracted and validated custom msas files path.
"""
extracted_paths = extract_files(paths)
supported_files = [item.value for item in SupportedCustomMSAFile]
for path in extracted_paths:
if path.suffix not in supported_files:
raise typer.BadParameter(
f"The file '{path}' is not supported. "
f"Only {supported_files} are supported for custom msas."
)
return extracted_paths
def validate_initial_guess(
initial_guess_file: Path | None,
) -> Path:
"""Extract and validate the file used for initial guess.
Args:
path (Path | None): Initial guess file parameter.
Raises:
typer.BadParameter: If a file is not supported.
Returns:
Path | None: Validated initial guess file path or None.
"""
if not initial_guess_file:
return None
supported_files = [
item.value for item in SupportedCustomTemplateFile
] # initial guess files are equivalent to template files
if initial_guess_file.suffix not in supported_files:
raise typer.BadParameter(
f"The file '{initial_guess_file}' is not supported. "
f"Only {supported_files} are supported for initial guess."
)
return initial_guess_file
def validate_template_mask(
template_mask_file: Path | None,
) -> Path:
"""Extract and validate the file used for template masks.g.
Args:
path (Path | None): template masks.g file parameter.
Raises:
typer.BadParameter: If a file is not supported.
Returns:
Path | None: Validated template masks.g file path or None.
"""
if not template_mask_file:
return None
supported_files = [
item.value for item in SupportedTemplateMaskFile
] # template masks.g files are equivalent to template files
if template_mask_file.suffix not in supported_files:
raise typer.BadParameter(
f"The file '{template_mask_file}' is not supported. "
f"Only {supported_files} are supported for template masks.g."
)
return template_mask_file
def validate_list_initial_guess(ig_files: list[Path]) -> list[Path]:
"""Extract and validate a list of initial guess files.
Args:
ig_files (list[Path]): List of initial guess files path.
Returns:
list[Path]: Extracted and validated initial guess files path.
"""
extracted_paths = extract_files(ig_files)
initial_guess_files = []
for path in extracted_paths:
validated_ig_path = validate_initial_guess(initial_guess_file=path)
if validated_ig_path:
initial_guess_files.append(validated_ig_path)
return initial_guess_files
def validate_list_template_mask(tm_files: list[Path]) -> list[Path]:
"""Extract and validate a list of template mask
Args:
tm_files (list[Path]): List of template mask files path.
Returns:
list[Path]: Extracted and validated template mask files path.
"""
extracted_paths = extract_files(tm_files)
template_mask_files = []
for path in extracted_paths:
validated_tm_path = validate_template_mask(template_mask_file=path)
if validated_tm_path:
template_mask_files.append(validated_tm_path)
return template_mask_files
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