def _get_embeddings_file_context(
file_manager: FileManagerInterface, result_kwargs: Dict[str, Any]
):
"""
:param file_manager: The FileManager derived class which will be used to create the file
:param result_kwargs: A dictionary which will be updated in-place to include the path to the newly created file
:return: a file context
"""
result_kwargs.setdefault("discard_per_amino_acid_embeddings", False)
if result_kwargs["discard_per_amino_acid_embeddings"] is True:
if result_kwargs.get("reduce", False) is False and result_kwargs.get("embeddings_transformer_function") is None:
raise InvalidParameterError(
"Cannot only have discard_per_amino_acid_embeddings: True. "
"Either also set `reduce: True` or define an `embeddings_transformer_function`, or both."
)
return nullcontext()
else:
embeddings_file_path = file_manager.create_file(
result_kwargs.get("prefix"),
result_kwargs.get("stage_name"),
"embeddings_file",
extension=".h5",
)
result_kwargs["embeddings_file"] = embeddings_file_path
return h5py.File(embeddings_file_path, "w")
def _get_transformed_embeddings_file_context(
file_manager: FileManagerInterface, result_kwargs: Dict[str, Any]
):
"""
:param file_manager: The FileManager derived class which will be used to create the file
:param result_kwargs: A dictionary which will be updated in-place to include the path to the newly created file
:return: a file context
"""
result_kwargs.setdefault("embeddings_transformer_function", None)
if result_kwargs["embeddings_transformer_function"] is not None:
transformed_embeddings_file_path = file_manager.create_file(
result_kwargs.get("prefix"),
result_kwargs.get("stage_name"),
"transformed_embeddings_file",
extension=".h5",
)
result_kwargs["transformed_embeddings_file"] = transformed_embeddings_file_path
return h5py.File(transformed_embeddings_file_path, "w")
return nullcontext()
def _get_reduced_embeddings_file_context(file_manager: FileManagerInterface,
result_kwargs: Dict[str, Any]):
"""
:param file_manager: The FileManager derived class which will be used to create the file
:param result_kwargs: A dictionary which will be updated in-place to include the path to the newly created file
:return: a file context
"""
# Create reduced embeddings file if set in params
result_kwargs.setdefault("reduce", False)
if result_kwargs["reduce"] is True:
reduced_embeddings_file_path = file_manager.create_file(
result_kwargs.get("prefix"),
result_kwargs.get("stage_name"),
"reduced_embeddings_file",
extension=".h5",
)
result_kwargs["reduced_embeddings_file"] = reduced_embeddings_file_path
return h5py.File(reduced_embeddings_file_path, "w")
return nullcontext()