def test_assembly_accessions():
"""Test NgdConfig.assembly_accessions getters/setters."""
config = NgdConfig()
assert config.assembly_accessions == []
config.assembly_accessions = "GCF_000203835.1"
assert config.assembly_accessions == ['GCF_000203835.1']
config.assembly_accessions = "GCF_000203835.1,GCF_000444875.1"
assert config.assembly_accessions == ['GCF_000203835.1', 'GCF_000444875.1']
def test_is_compatible_assembly_accession():
"""Test NgdConfig.is_compatible_assembly_accession."""
config = NgdConfig()
assert config.is_compatible_assembly_accession("GCF_000444875.1")
config.assembly_accessions = "GCF_000203835.1,GCF_000444875.1"
assert config.is_compatible_assembly_accession("GCF_000444875.1")
config.assembly_accessions = "GCF_000203835.1"
assert not config.is_compatible_assembly_accession("GCF_000444875.1")
def test_file_formats():
"""Test NgdConfig.file_formats getters/setters."""
config = NgdConfig()
assert config.file_formats == ['genbank']
config.file_formats = ['genbank', 'fasta']
assert config.file_formats == ['genbank', 'fasta']
config.file_formats = "all"
assert config.file_formats == list(NgdConfig._FORMATS)
with pytest.raises(ValueError):
config.file_formats = "garbage"
def test_group():
"""Test NgdConfig.group getters/setters."""
config = NgdConfig()
assert config.group == SUPPORTED_TAXONOMIC_GROUPS
config.group = ['bacteria', 'fungi']
assert config.group == ['bacteria', 'fungi']
config.group = "all"
assert config.group == SUPPORTED_TAXONOMIC_GROUPS
with pytest.raises(ValueError):
config.group = "garbage"
def test_is_compatible_assembly_level():
"""Test NgdConfig.is_compatible_assembly_level."""
config = NgdConfig()
ncbi_string = "Complete Genome"
assert config.is_compatible_assembly_level(ncbi_string)
config.assembly_levels = "complete"
assert config.is_compatible_assembly_level(ncbi_string)
config.assembly_levels = "chromosome,complete"
assert config.is_compatible_assembly_level(ncbi_string)
config.assembly_levels = "chromosome"
assert not config.is_compatible_assembly_level(ncbi_string)
def test_init():
"""Test NgdConfig initialises with the correct default values."""
config = NgdConfig()
for key in NgdConfig._DEFAULTS:
expected = NgdConfig._DEFAULTS[key]
if key in NgdConfig._LIST_TYPES:
if expected:
if expected[0] == 'all':
expected = expected[1:]
else:
expected = expected[:1]
if 'all' in expected:
expected = expected[::].remove('all')
elif isinstance(expected, list):
expected = expected[0]
assert getattr(config, key) == expected
def test_groups():
"""Test NgdConfig.groups getters/setters."""
config = NgdConfig()
assert config.groups == SUPPORTED_TAXONOMIC_GROUPS
config.groups = ['bacteria', 'fungi']
assert config.groups == ['bacteria', 'fungi']
config.groups = "all"
assert config.groups == SUPPORTED_TAXONOMIC_GROUPS
with pytest.raises(ValueError):
config.groups = "garbage"
# No metagenomes in refseq
with pytest.raises(ValueError):
config.section = "refseq"
config.groups = "metagenomes"
# genbank has metagenomes
config.section = "genbank"
config.groups = "metagenomes"
def test_assembly_levels():
"""Test NgdConfig.assembly_levels getters/setters."""
config = NgdConfig()
with pytest.raises(ValueError):
config.assembly_levels = 'garbage'
def test_section():
"""Test NgdConfig.section getters/setters."""
config = NgdConfig()
with pytest.raises(ValueError):
config.section = 'garbage'
def test_type_materials():
"""Test NgdConfig.type_materials setters."""
config = NgdConfig()
with pytest.raises(ValueError):
config.type_materials = "invalid"
def test_refseq_categories():
"""Test NgdConfig.refseq_categories getters/setters."""
config = NgdConfig()
with pytest.raises(ValueError):
config.refseq_categories = 'garbage'
