bioprov package¶
Subpackages¶
- bioprov.data package
- bioprov.programs package
- bioprov.src package
- bioprov.tests package
- Submodules
- bioprov.tests.test_bioprov_imports module
- bioprov.tests.test_bioprov_integration module
- bioprov.tests.test_bioprov_programs module
- bioprov.tests.test_bioprov_workflows module
- bioprov.tests.test_src_config module
- bioprov.tests.test_src_file module
- bioprov.tests.test_src_main module
- bioprov.tests.test_src_prov module
- Module contents
- bioprov.workflows package
Submodules¶
bioprov.bioprov module¶
BioProv command-line application. This module holds the main executable.
- class bioprov.bioprov.CommandOptionsParser¶
Bases:
object
- __init__()¶
- classmethod clear_db()¶
- classmethod create_provstore()¶
- classmethod list()¶
- classmethod show_config()¶
- classmethod show_db()¶
- classmethod show_provstore()¶
- classmethod version()¶
- bioprov.bioprov.main(args=None)¶
Main function to run the BioProv command-line application. Calls the subparsers defined in the Workflows module.
- Parameters
args – args to call the function with. Usually is None and args are automatically extracted from the command line. Passing args is used for testing only.
bioprov.utils module¶
Helper functions.
- bioprov.utils.assert_tax_rank(tax_rank)¶
Tests if a string is a valid taxonomic rank. :param tax_rank: String to be evaluated. :return: True or False.
- bioprov.utils.build_prov_attributes(dictionary, namespace)¶
Inserting attributes into a Provenance object can be tricky. We need a NameSpace for said object, and attributes must be named correctly. This helper function builds a dictionary of attributes properly formatted to be inserted into a namespace.
- Parameters
dictionary – dict with object attributes.
namespace – instance of Namespace.
- Returns
List of tuples (QualifiedName, value)
- bioprov.utils.convert_bytes(num)¶
Helper function to convert bytes into KB, MB, etc. From https://stackoverflow.com/questions/2104080/how-can-i-check-file-size-in-python
- Parameters
num – Number of bytes.
- bioprov.utils.create_logger(log_level=20, log_file=None, tag=None)¶
- bioprov.utils.dict_to_sha256(dictionary)¶
Get sha256 hexdigest from a dictionary :param dictionary: dict :return: hexdigest
- bioprov.utils.dict_to_string(dictionary)¶
Converts a dictionary to string for pretty printing :param dictionary: dict :return: str
- bioprov.utils.file_to_sha256(path)¶
Get the sha256 of file. Returns None if it does not exist. :param path: A valid file path. :return: sha256 digest or None.
- bioprov.utils.get_size(path, convert=True)¶
Calculate size of a given file. :param path: Valid _path of a file. :param convert: Whether to convert the values to bytes, KB, etc. :return: Size with converted values. 0 if file does not exist.
- bioprov.utils.has_serializer(object_)¶
- bioprov.utils.is_serializable_type(type_)¶
- bioprov.utils.parser_help(parser)¶
Shows help if no arguments are passed for parser. :param parser: An instance of argparse.ArgumentParser :return:
- bioprov.utils.pattern_replacer(pattern, iterable_of_olds, new)¶
Replaces a list of old terms from a given pattern for a new term.
Used for switching file paths in the ‘bioprov.src.main.from_json’ module.
- Parameters
pattern – pattern to replace.
iterable_of_olds – old terms.
new – new term.
- Returns
- bioprov.utils.serializer(object_)¶
Helper function to serialize objects into JSON compatible dictionaries. :param object_: A BioProv class instance. :return: JSON compatible dictionary.
- bioprov.utils.serializer_filter(_object, keys)¶
Filters keys from _object.__dict__ to make custom serializers.
- Parameters
_object – A bioprov object
keys – keys to be filtered.
- Returns
dict
Module contents¶
Init module for package bioprov.
Inherits objects from the src/ package.