pyalma.fileReader.FileReader

class documentation

class FileReader:

Known subclasses: pyalma.local.LocalFileReader, pyalma.ssh.SshClient

Constructor: FileReader()

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Abstract base class for reading and managing different file types, both locally and remotely.

This class is designed to be subclassed by specific implementations (e.g., local or SSH).

Method __del__ Destructor to clean up temporary files if clean_on_destruction is enabled.
Method __init__ Initializes the FileReader with default configurations.
Method clean_tmp_files Deletes a temporary file if it exists.
Method decode_content_by_type Decodes content based on file type, returning a DataFrame or raw string.
Method download_remote_file Abstract method. Downloads a file from a remote location.
Method get_file_extension Extracts the file extension from a given path.
Method get_file_size Placeholder to get file size.
Method is_remote Checks if the reader is set to remote mode.
Method isfile Checks if a given path exists and is a file.
Method listdir Abstract method. Should be implemented by subclasses to list directory contents.
Method load_h5ad_file Placeholder for remote/local logic in loading H5AD files.
Method read_file Unified file reader for local or remote paths. :param path: File path. :param type: Optional file type override (generic types: pdf, image, text, csv, zip). :param as_dataframe: Whether to parse into a DataFrame...
Method read_file_into_df File reader into a dataframe for local and remote paths :param path: File path. :param type: Optional file type override (generic types: pdf, image, text, csv, zip). :param as_dataframe: Force a parsing into a DataFrame...
Method read_h5ad Reads an H5AD file using `anndatareader`.
Method read_vcf_file_into_df Reads a VCF (Variant Call Format) file using `pysam`.
Method set_clean_on_dest Sets the `clean_on_destruction` flag.
Method write_to_remote_file Abstract method. Writes data to a remote file.
Instance Variable clean_on_destruction Undocumented
Instance Variable files_to_clean Undocumented
Instance Variable remote Undocumented
Method _is_auto_dataframe_type Undocumented
Method _is_binary_type Undocumented
Method _is_text_type Undocumented
def __del__(self):
overridden in pyalma.ssh.SshClient

Destructor to clean up temporary files if clean_on_destruction is enabled.

def __init__(self):
overridden in pyalma.local.LocalFileReader, pyalma.ssh.SshClient

Initializes the FileReader with default configurations.

  • `files_to_clean`: Tracks temporary files that may need deletion.
  • `remote`: Flag indicating remote operation.
  • `clean_on_destruction`: Determines whether to delete files on object destruction.
def clean_tmp_files(self, path):

Deletes a temporary file if it exists.

:param path: Path to the file to delete. :type path: str

def decode_content_by_type(self, content, type, as_dataframe=False, as_binary=False, **kwargs):

Decodes content based on file type, returning a DataFrame or raw string.

:param content: Raw content (str, bytes, or file path). :param type: File type (file extension generic types: pdf, image, text, csv, zip). :param kwargs: Extra arguments for `pandas.read_csv`. :return: Decoded content (DataFrame, str, or bytes).

def download_remote_file(self, remote_path, local_path):
overridden in pyalma.ssh.SshClient

Abstract method. Downloads a file from a remote location.

:raises NotImplementedError: Always.

def get_file_extension(self, file_path):

Extracts the file extension from a given path.

:param file_path: Full path to the file. :type file_path: str

:return: File extension without the dot. :rtype: str

def get_file_size(self, path):
overridden in pyalma.ssh.SshClient

Placeholder to get file size.

:param path: Path to the file. :type path: str

:return: File size (to be implemented). :rtype: None

def is_remote(self):

Checks if the reader is set to remote mode.

:return: True if remote, False otherwise. :rtype: bool

def isfile(self, path):
overridden in pyalma.ssh.SshClient

Checks if a given path exists and is a file.

:param path: Path to check. :type path: str

:return: True if path exists and is a file. :rtype: bool

def listdir(self, path):
overridden in pyalma.local.LocalFileReader, pyalma.ssh.SshClient

Abstract method. Should be implemented by subclasses to list directory contents.

:raises NotImplementedError: Always.

def load_h5ad_file(self, path, local_path):
overridden in pyalma.ssh.SshClient

Placeholder for remote/local logic in loading H5AD files.

:param path: Path to the file. :param local_path: Local destination path. :type path: str :type local_path: str

:return: Path to use. :rtype: str

def read_file(self, path, type=None, as_dataframe=False, as_binary=False, **kwargs):

Unified file reader for local or remote paths. :param path: File path. :param type: Optional file type override (generic types: pdf, image, text, csv, zip). :param as_dataframe: Whether to parse into a DataFrame. :param as_binary: Force raw binary return.

def read_file_into_df(self, path, type=None, as_binary=False, **kwargs):

File reader into a dataframe for local and remote paths :param path: File path. :param type: Optional file type override (generic types: pdf, image, text, csv, zip). :param as_dataframe: Force a parsing into a DataFrame. :param as_binary: Force raw binary return.

def read_h5ad(self, path):

Reads an H5AD file using `anndatareader`.

:param path: Path to the `.h5ad` file. :type path: str

:return: Loaded `AnnData` object. :rtype: AnnData

def read_vcf_file_into_df(self, path):

Reads a VCF (Variant Call Format) file using `pysam`.

:param path: Path to the VCF file. :type path: str

:return: VCF file as a `pysam.VariantFile` object. :rtype: pysam.VariantFile

def set_clean_on_dest(self, value):

Sets the `clean_on_destruction` flag.

:param value: Enable or disable automatic cleanup. :type value: bool

def write_to_remote_file(self, data, remote_path, file_format='csv'):
overridden in pyalma.ssh.SshClient

Abstract method. Writes data to a remote file.

:param data: Data to write. :param remote_path: Path on remote server. :param file_format: File format, default is 'csv'. :raises NotImplementedError: Always.

clean_on_destruction =

Undocumented

files_to_clean: list =

Undocumented

remote: bool =
overridden in pyalma.ssh.SshClient

Undocumented

def _is_auto_dataframe_type(self, type):

Undocumented

def _is_binary_type(self, type):

Undocumented

def _is_text_type(self, type):

Undocumented