Module `psdi_data_conversion.converters.example.converter`

@file psdi_data_conversion/converters/example/converter.py

Example file converter

Functions

def process_example_option(l_opts: list[str] | None) ‑> dict[str, str]

Expand source code

def process_example_option(l_opts: list[str] | None) -> dict[str, str]:
    """Example method to process an option for this converter"""
    if l_opts is None:
        return {"opt": "None"}
    if len(l_opts) == 1:
        return {"opt": l_opts[0]}
    if len(l_opts) == 2:
        return {l_opts[0]: l_opts[1]}
    raise FileConverterArgException("Invalid number of arguments for option '--example-opt'")

Example method to process an option for this converter

Classes

class ExampleFileConverter (filename: str, to_format: str, from_format: str | None = None, data: dict[str, typing.Any] | None = None, abort_callback: Callable[[int], None] = <function abort_raise>, use_envvars=False, input_dir='./psdi_data_conversion/static/uploads', output_dir='./psdi_data_conversion/static/downloads', no_clobber=False, max_file_size=None, no_check=False, log_file: str | None = None, log_mode='full', log_level: int | None = None, refresh_local_log: bool = True, delete_input=False)

Expand source code

class ExampleFileConverter(FileConverter):
    """File converter specialised to use Example for conversions"""

    meta: FileConverterMeta = FileConverterMeta.load(__file__)
    has_in_format_flags_or_options = True
    has_out_format_flags_or_options = True

    allowed_flags = (("--example-flag-1",
                      "(Example converter only). Help text for example flag 1."),
                     ("--example-flag-2",
                     "(Example converter only). Help text for example flag 2."))
    allowed_options = (("--example-opt",
                        {"help": "(Example converter only). Help text for example option.",
                         "type": str,
                         "default": None,
                         "nargs": "+"},
                        process_example_option))

    def _convert(self):
        """Mandatory override: Perform the conversion"""
        pass

    def _create_message(self) -> str:
        """Optional override: Create a log of options passed to the converter"""
        return ""

File converter specialised to use Example for conversions

Initialize the object, storing needed data and setting up loggers.

Parameters

filename : str: The filename of the input file to be converted, either relative to current directory or fully-qualified
to_format : str: The desired format to convert to, as the file extension (e.g. "cif")
from_format : str | None: The format to convert from, as the file extension (e.g. "pdb"). If None is provided (default), will be determined from the extension of filename
data : dict[str | Any] | None: A dict of any other data needed by a converter or for extra logging information, default empty dict. See the docstring of each converter for supported keys and values that can be passed to data here
abort_callback : Callable[[int], None]: Function to be called if the conversion hits an error and must be aborted, default abort_raise, which raises an appropriate exception
use_envvars : bool: If set to True, environment variables will be checked for any that set options for this class and used, default False
input_dir : str: The location of input files relative to the current directory
output_dir : str: The location of output files relative to the current directory
max_file_size : float: The maximum allowed file size for input/output files, in MB. If 0, will be unlimited. Default 0 (unlimited)
no_check : bool: If False (default), will check at setup whether or not a conversion between the desired file formats is supported with the specified converter
log_file : str | None: If provided, all logging will go to a single file or stream. Otherwise, logs will be split up among multiple files for server-style logging.
log_mode : str: How logs should be stores. Allowed values are: - 'full' - Multi-file logging, only recommended when running as a public web app - 'full-force' - Multi-file logging, only recommended when running as a public web app, with the log file name forced to be used for the output log - 'simple' - Logs saved to one file - 'stdout' - Output logs and errors only to stdout - 'none' - Output only errors to stdout
log_level : int | None: The level to log output at. If None (default), the level will depend on the chosen log_mode: - 'full', 'full-force', or 'simple': INFO - 'stdout' - INFO to stdout, no logging to file - 'none' - ERROR to stdout, no logging to file
refresh_local_log : bool: If True, the local log generated from this run will be overwritten. If False it will be appended to. Default True
delete_input : bool: Whether or not to delete input files after conversion, default False

Ancestors

FileConverter

Class variables

var allowed_flags : tuple[tuple[str, dict, collections.abc.Callable], ...] | None
var allowed_options : tuple[tuple[str, dict, collections.abc.Callable], ...] | None
var has_in_format_flags_or_options
var has_out_format_flags_or_options
var meta : FileConverterMeta

class converter (filename: str, to_format: str, from_format: str | None = None, data: dict[str, typing.Any] | None = None, abort_callback: Callable[[int], None] = <function abort_raise>, use_envvars=False, input_dir='./psdi_data_conversion/static/uploads', output_dir='./psdi_data_conversion/static/downloads', no_clobber=False, max_file_size=None, no_check=False, log_file: str | None = None, log_mode='full', log_level: int | None = None, refresh_local_log: bool = True, delete_input=False)

Expand source code

class ExampleFileConverter(FileConverter):
    """File converter specialised to use Example for conversions"""

    meta: FileConverterMeta = FileConverterMeta.load(__file__)
    has_in_format_flags_or_options = True
    has_out_format_flags_or_options = True

    allowed_flags = (("--example-flag-1",
                      "(Example converter only). Help text for example flag 1."),
                     ("--example-flag-2",
                     "(Example converter only). Help text for example flag 2."))
    allowed_options = (("--example-opt",
                        {"help": "(Example converter only). Help text for example option.",
                         "type": str,
                         "default": None,
                         "nargs": "+"},
                        process_example_option))

    def _convert(self):
        """Mandatory override: Perform the conversion"""
        pass

    def _create_message(self) -> str:
        """Optional override: Create a log of options passed to the converter"""
        return ""

File converter specialised to use Example for conversions

Initialize the object, storing needed data and setting up loggers.

Parameters

filename : str: The filename of the input file to be converted, either relative to current directory or fully-qualified
to_format : str: The desired format to convert to, as the file extension (e.g. "cif")
from_format : str | None: The format to convert from, as the file extension (e.g. "pdb"). If None is provided (default), will be determined from the extension of filename
data : dict[str | Any] | None: A dict of any other data needed by a converter or for extra logging information, default empty dict. See the docstring of each converter for supported keys and values that can be passed to data here
abort_callback : Callable[[int], None]: Function to be called if the conversion hits an error and must be aborted, default abort_raise, which raises an appropriate exception
use_envvars : bool: If set to True, environment variables will be checked for any that set options for this class and used, default False
input_dir : str: The location of input files relative to the current directory
output_dir : str: The location of output files relative to the current directory
max_file_size : float: The maximum allowed file size for input/output files, in MB. If 0, will be unlimited. Default 0 (unlimited)
no_check : bool: If False (default), will check at setup whether or not a conversion between the desired file formats is supported with the specified converter
log_file : str | None: If provided, all logging will go to a single file or stream. Otherwise, logs will be split up among multiple files for server-style logging.
log_mode : str: How logs should be stores. Allowed values are: - 'full' - Multi-file logging, only recommended when running as a public web app - 'full-force' - Multi-file logging, only recommended when running as a public web app, with the log file name forced to be used for the output log - 'simple' - Logs saved to one file - 'stdout' - Output logs and errors only to stdout - 'none' - Output only errors to stdout
log_level : int | None: The level to log output at. If None (default), the level will depend on the chosen log_mode: - 'full', 'full-force', or 'simple': INFO - 'stdout' - INFO to stdout, no logging to file - 'none' - ERROR to stdout, no logging to file
refresh_local_log : bool: If True, the local log generated from this run will be overwritten. If False it will be appended to. Default True
delete_input : bool: Whether or not to delete input files after conversion, default False

Ancestors

FileConverter

Class variables

var has_in_format_flags_or_options
var has_out_format_flags_or_options

Inherited members

FileConverter:
- allowed_flags
- allowed_options
- can_be_registered
- database_key_prefix
- desc
- from_format_name
- get_in_format_flags
- get_in_format_options
- get_out_format_flags
- get_out_format_options
- get_quality
- id
- info
- meta
- name
- run
- supports_ambiguous_extensions
- to_format_name
- url
- uuid