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improve argument CI tests
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@oschwengers
oschwengers committed Nov 25, 2021
1 parent 4c92cf8 commit f5c57ef
Showing 1 changed file with 57 additions and 13 deletions.
70 changes: 57 additions & 13 deletions test/test_args.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
)
def test_genome_failing(parameters, tmpdir):
# test genome arguments
cmd_line = ['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters
cmd_line = ['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS
proc = run(cmd_line)
assert proc.returncode != 0

Expand All @@ -36,7 +36,7 @@ def test_genome_failing(parameters, tmpdir):
def test_database_failing_parameter(parameters, tmpdir):
# test database arguments

cmd_line = ['bin/bakta', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna']
cmd_line = ['bin/bakta', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna']
proc = run(cmd_line)
assert proc.returncode != 0

Expand Down Expand Up @@ -88,7 +88,7 @@ def test_output_failing():
)
def test_tmp_dir_failiing(parameters, tmpdir):
# test tmp dir arguments
cmd_line = ['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna']
cmd_line = ['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna']
proc = run(cmd_line)
assert proc.returncode != 0

Expand All @@ -111,7 +111,7 @@ def test_tmp_dir_ok(tmpdir):
)
def test_prodigal_tf_failiing(parameters, tmpdir):
# test prodigal training file arguments
cmd_line = ['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna']
cmd_line = ['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna']
proc = run(cmd_line)
assert proc.returncode != 0

Expand Down Expand Up @@ -139,7 +139,7 @@ def test_prodigal_tf_ok(tmpdir):
)
def test_replicons_failiing(parameters, tmpdir):
# test replicons file arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna'])
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode != 0


Expand Down Expand Up @@ -174,7 +174,7 @@ def test_replicons_ok(tmpdir):
)
def test_proteins_failiing(parameters, tmpdir):
# test proteins file arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna'])
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode != 0


Expand All @@ -197,31 +197,75 @@ def test_proteins_ok(tmpdir):
(['--locus', '']), # empty
(['--locus', ' ']), # whitespace only
(['--locus', ' ']), # whitespaces only
(['--locus', 'fo o']) # containing whitespace
(['--locus', 'fo o']), # containing whitespace
(['--locus', 'ABCDEFGHIJKLMNOPQRSTU']) # more than 20 characters
]
)
def test_locus_failiing(parameters, tmpdir):
# test locus prefix arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna'])
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode != 0


@pytest.mark.slow
@pytest.mark.parametrize(
'parameters',
[
(['--locus', 'ABC']),
(['--locus', 'ABCDEFGHIJKLMNOPQRST']),
(['--locus', 'A123_.:*#-'])
]
)
def test_locus_ok(parameters, tmpdir):
# test locus prefix arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode == 0


@pytest.mark.parametrize(
'parameters',
[
(['--locus-tag']), # not provided
(['--locus-tag', '']), # empty
(['--locus-tag', ' ']), # whitespace only
(['--locus-tag', ' ']), # whitespaces only
(['--locus-tag', 'fo o']) # containing whitespace
(['--locus-tag', 'fo o']), # containing whitespace
(['--locus-tag', '123ABC']), # first character is not a letter
(['--locus-tag', 'abc']), # lower case letters
(['--locus-tag', 'AB']), # less than 3 characters
(['--locus-tag', 'ABCDEFGHIJKLM']), # more than 12 characters
(['--locus-tag', 'ABC_']), # wrong characters
(['--locus-tag', 'ABC-']), # wrong characters
(['--locus-tag', 'ABC!']), # wrong characters
(['--locus-tag', 'ABC?']), # wrong characters
(['--locus-tag', 'ABC*']), # wrong characters
(['--locus-tag', 'ABC.']), # wrong characters
(['--locus-tag', 'ABC,']), # wrong characters
(['--locus-tag', 'ABC;']) # wrong characters
]
)
def test_locustag_failiing(parameters, tmpdir):
# test locus-tag prefix arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna'])
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode != 0


@pytest.mark.slow
@pytest.mark.parametrize(
'parameters',
[
(['--locus-tag', 'ABC']),
(['--locus-tag', 'ABCDEFGHIJKL']),
(['--locus-tag', 'A12']),
(['--locus-tag', 'A23456789012'])
]
)
def test_locustag_ok(parameters, tmpdir):
# test locus-tag prefix arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode == 0


@pytest.mark.parametrize(
'parameters',
[
Expand All @@ -233,7 +277,7 @@ def test_locustag_failiing(parameters, tmpdir):
)
def test_genus_failiing(parameters, tmpdir):
# test genus prefix arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna'])
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode != 0


Expand All @@ -248,7 +292,7 @@ def test_genus_failiing(parameters, tmpdir):
)
def test_species_failiing(parameters, tmpdir):
# test species prefix arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna'])
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode != 0


Expand All @@ -263,7 +307,7 @@ def test_species_failiing(parameters, tmpdir):
)
def test_strain_failiing(parameters, tmpdir):
# test strain prefix arguments
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + ['test/data/NC_002127.1.fna'])
proc = run(['bin/bakta', '--db', 'test/db', '--output', tmpdir] + parameters + SKIP_PARAMETERS + ['test/data/NC_002127.1.fna'])
assert proc.returncode != 0


Expand Down

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