def test_registry():
rr = Registry()
assert rr.conversion_exists("bam", "bed") is True
assert rr.conversion_exists("bam", "dummy") is False
assert ('.bam', '.bed') in rr
assert ('.nimport', '.naoik') not in rr
converter = rr[('.bam', '.bed')]
with pytest.raises(KeyError) as err:
rr[('.bam', '.bed')] = converter
assert "'an other converter already exist for .bam -> .bed'" == str(
err.value)
def test_registry_with_dependencies():
rr = Registry()
assert rr.conversion_exists(("BAM", ), ("COV", ))
assert not rr.conversion_exists(("BAM", ), ("DUMMY", ))
assert rr.conversion_exists(("BIGWIG", ), ("COV", ), allow_indirect=True)
assert (('BAM', ), ('COV', )) in rr
assert (('NIMPORT', ), ('NAOIK', )) not in rr
converter = rr[('BAM', ), ('COV', )]
with pytest.raises(KeyError) as err:
rr[('BAM', ), ('COV', )] = converter
assert (str(
err.value) == "'an other converter already exists for BAM -> COV'")
def test_registry_with_less_dependencies():
rr = Registry()
# Isnt'it supposed to be upper case?
# assert rr.conversion_exists("bam", "bed") is True
# assert rr.conversion_exists("bam", "dummy") is False
assert rr.conversion_exists("FASTQ", "FASTA")
assert not rr.conversion_exists("BAM", "DUMMY")
assert rr.conversion_exists("CLUSTAL", "FASTQ", allow_indirect=True)
assert ('FASTQ', 'FASTA') in rr
assert ('NIMPORT', 'NAOIK') not in rr
converter = rr[('FASTQ', 'FASTA')]
with pytest.raises(KeyError) as err:
rr[('FASTQ', 'FASTA')] = converter
assert (str(
err.value) == "'an other converter already exists for FASTQ -> FASTA'")
def test_registry():
rr = Registry()
# Isnt'it supposed to be upper case?
# assert rr.conversion_exists("bam", "bed") is True
# assert rr.conversion_exists("bam", "dummy") is False
assert rr.conversion_exists("BAM", "BED")
assert not rr.conversion_exists("BAM", "DUMMY")
assert rr.conversion_exists("SRA", "BAM", allow_indirect=True)
assert ('BAM', 'BED') in rr
assert ('NIMPORT', 'NAOIK') not in rr
converter = rr[('BAM', 'BED')]
with pytest.raises(KeyError) as err:
rr[('BAM', 'BED')] = converter
assert (str(err.value)
== "'an other converter already exists for BAM -> BED'")
def test_registry_with_less_dependencies():
rr = Registry()
assert rr.conversion_exists(("FASTQ", ), ("FASTA", ))
assert not rr.conversion_exists(("BAM", ), ("DUMMY", ))
assert rr.conversion_exists(("CLUSTAL", ), ("FASTQ", ),
allow_indirect=True)
# one to one
assert (('FASTQ', ), ('FASTA', )) in rr
# unexisting entry
assert (('NIMPORT', ), ('NAOIK', )) not in rr
# one to many
assert (('FASTQ', ), ('FASTA', 'QUAL')) in rr
# without tuples
assert ['FASTQ', 'FASTA'] in rr
assert [('FASTQ', ), 'FASTA'] in rr
assert [['FASTQ'], 'FASTA'] in rr
assert [['FASTQ'], ['FASTA']] in rr
assert ['FASTQ', ('FASTA', )] in rr
# argument must be a list or tuple
try:
'FASTA' in rr
assert False
except ValueError:
assert True
# must have 2 items only
try:
['a', 'b', 'c'] in rr
assert False
except ValueError:
assert True
# iterator through the conversions
for this in rr:
assert this
converter = rr[('FASTQ', ), ('FASTA', )]
with pytest.raises(KeyError) as err:
rr[('FASTQ', ), ('FASTA', )] = converter
assert (str(
err.value) == "'an other converter already exists for FASTQ -> FASTA'")
