def get_genome_group(src_loc: Path, config: Config) -> GenomeGroup:
"""Get the ``GenomeGroup`` based on ``src_loc`` and ``config``.
``Config`` is used to set global filter codes and exclude files on group creation.
Args:
src_loc: Path, can be directory or file
config: the running config object
Returns:
``GenomeGroup`` based on ``src_loc`` and config.
"""
ggrp = GenomeGroup()
# check if src_loc is a single file, otherwise assume it's a directory
if src_loc.is_file():
ggrp.add_file(source_file=src_loc)
else:
ggrp.add_folder(source_folder=src_loc,
exclude_files=config.exclude_files,
ignore_test_files=True)
if config.filter_codes:
LOGGER.info("Category restriction, chosen categories: %s",
sorted(config.filter_codes))
ggrp.set_filter(filter_codes=config.filter_codes)
for k, genome in ggrp.items():
LOGGER.info(
"%s",
colorize_output(
f"{len(genome.targets)} mutation targets found in {genome.source_file} AST.",
"green" if len(genome.targets) > 0 else "yellow",
),
)
for e in config.exclude_files:
LOGGER.info("%s", colorize_output(f"{e.resolve()} excluded.",
"yellow"))
return ggrp
def test_GenomeGroup_basic_properties(binop_file, boolop_file, compare_file):
"""Basic class property tests and dictionary manipulation."""
ggrp = GenomeGroup(binop_file)
ggrp.add_file(boolop_file)
ggrp.add_file(compare_file)
# test ValuesView is iterable view.
for v in ggrp.values():
assert isinstance(v, Genome)
# test basic __iter__ property
keys = [k for k in ggrp]
assert len(keys) == 3
# __repr__ is a string representation of the store
assert isinstance(ggrp.__repr__(), str)
# test basic .items() method, uses .pop() to activate __del__
key_values = [(k, v) for k, v in ggrp.items()]
for k, v in key_values:
v2 = ggrp.pop(k)
assert v2 == v
