def test_build_indices_false_no_such_rrna_index_prefix(tmpdir):
"""
Test that :py:const:`riboviz.params.BUILD_INDICES` is false
and no such files with prefixe
:py:const:`riboviz.params.RRNA_INDEX_PREFIX` returns a non-zero
exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
index_dir = tmpdir.mkdir("index")
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.BUILD_INDICES] = False
# Cast index_dir to string. If not done, then, when config is saved
# the value will be
# !!python/object:py._path.local.LocalPath
# strpath: /tmp/.../index
# Casting to string gives the value /tmp/.../index/ as desired.
config[params.INDEX_DIR] = str(index_dir)
# Create empty file for ORF index prefix, so check for that
# file will succeed.
index_file = index_dir.join(hisat2.HT2_FORMAT.format(
config[params.ORF_INDEX_PREFIX], 1))
with open(index_file, 'w') as f:
pass
config[params.RRNA_INDEX_PREFIX] = "NoSuchRrnaPrefix"
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_build_indices_false_no_such_rrna_index_prefix(tmp_file, tmp_dir):
"""
Test that :py:const:`riboviz.params.BUILD_INDICES` is false
and no such files with prefixe
:py:const:`riboviz.params.RRNA_INDEX_PREFIX` returns a non-zero
exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
:param tmp_dir: Path to temporary directory
:type tmp_dir: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.BUILD_INDICES] = False
config[params.INDEX_DIR] = tmp_dir
# Create empty file with ORF index prefix, so check for that
# file will succeed.
with open(
os.path.join(
tmp_dir,
hisat2.HT2_FORMAT.format(config[params.ORF_INDEX_PREFIX], 1)),
'w') as f:
pass
config[params.RRNA_INDEX_PREFIX] = "NoSuchRrnaPrefix"
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_environment_var_not_found(env):
"""
Test that a workflow with an environment variable pointing
to a non-existent path raises a non-zero exit code.
:param env: Environment variable
:type env: str or unicode
"""
exit_code = run_nextflow(riboviz.test.VIGNETTE_CONFIG,
envs={env: "noSuchDirectory"},
validate_only=True)
assert exit_code != 0, "Unexpected exit code %d" % exit_code
def test_environment_vars(tmpdir):
"""
Test that a workflow with environment variables,
:py:const:`riboviz.params.ENV_DIRS`, validates.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
envs = {env: tmpdir for env in params.ENV_DIRS}
exit_code = run_nextflow(riboviz.test.VIGNETTE_CONFIG,
envs=envs,
validate_only=True)
assert exit_code == 0, "Unexpected exit code %d" % exit_code
def prep_riboviz_fixture(skip_workflow_fixture, config_fixture):
"""
Run :py:const:`riboviz.test.NEXTFLOW_WORKFLOW` (via Nextflow)
if ``skip_workflow_fixture`` is not ``True``.
:param skip_workflow_fixture: Should workflow not be run?
:type skip_workflow_fixture: bool
:param config_fixture: Configuration file
:type config_fixture: str or unicode
"""
if not skip_workflow_fixture:
env_vars = environment.get_environment_vars()
exit_code = nextflow.run_nextflow(config_fixture, envs=env_vars)
assert exit_code == 0, \
"prep_riboviz returned non-zero exit code %d" % exit_code
def test_fq_files_not_found(tmp_file):
"""
Test that non-existent :py:const:`riboviz.params.FQ_FILES` files
raise a non-zero exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.FQ_FILES] = {"foo1": "foo1.fq", "foo2": "foo2.fq"}
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_sample_sheet_not_found(tmp_file):
"""
Test that providing :py:const:`riboviz.params.MULTIPLEX_FQ_FILES`
and a non-existent :py:const:`riboviz.params.SAMPLE_SHEET` file
returns a non-zero exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
"""
with open(riboviz.test.SIMDATA_MULTIPLEX_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.SAMPLE_SHEET] = "foo.tsv"
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_dir_in_not_found(tmpdir):
"""
Test that a non-existent :py:const:`riboviz.params.INPUT_DIR`
directory raises a non-zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.INPUT_DIR] = "foo"
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_extract_umis_no_umi_regexp(tmp_file):
"""
Test that if :py:const:`riboviz.params.EXTRACT_UMIS` is `TRUE`
but no :py:const:`riboviz.params.UMI_REGEXP` returns a non-zero
exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
"""
with open(riboviz.test.SIMDATA_UMI_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
del config[params.UMI_REGEXP]
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_extract_umis_no_umi_regexp(tmpdir):
"""
Test that if :py:const:`riboviz.params.EXTRACT_UMIS` is `TRUE`
but no :py:const:`riboviz.params.UMI_REGEXP` returns a non-zero
exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.SIMDATA_UMI_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
del config[params.UMI_REGEXP]
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_multiplex_fq_files_not_found(tmpdir):
"""
Test that non-existent
:py:const:`riboviz.params.MULTIPLEX_FQ_FILES`
files raise a non-zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.SIMDATA_MULTIPLEX_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.MULTIPLEX_FQ_FILES] = ["foo1.fq", "foo2.fq"]
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_sample_sheet_not_found(tmpdir):
"""
Test that providing :py:const:`riboviz.params.MULTIPLEX_FQ_FILES`
and a non-existent :py:const:`riboviz.params.SAMPLE_SHEET` file
returns a non-zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.SIMDATA_MULTIPLEX_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.SAMPLE_SHEET] = "foo.tsv"
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_max_read_length_less_min(tmp_file):
"""
Test that :py:const:`riboviz.params.MAX_READ_LENGTH` less than
:py:const:`riboviz.params.MIN_READ_LENGTH` returns a non-zero exit
code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.MIN_READ_LENGTH] = 10
config[params.MAX_READ_LENGTH] = 9
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_no_sample_multiplex_fq_files(tmp_file):
"""
Test that missing :py:const:`riboviz.params.FQ_FILES` and
:py:const:`riboviz.params.MULTIPLEX_FQ_FILES` returns a non-zero
exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.FQ_FILES] = []
config[params.MULTIPLEX_FQ_FILES] = []
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_build_indices_false_no_such_index_dir(tmp_file):
"""
Test that :py:const:`riboviz.params.BUILD_INDICES` is false
and no such index directory :py:const:`riboviz.params.INDEX_DIR`
returns a non-zero exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.BUILD_INDICES] = False
config[params.INDEX_DIR] = "NoSuchDirectory"
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_invalid_value(tmpdir, parameter):
"""
Test that providing invalid values for a parameter returns a
non-zero exit code.
:param parameter: Parameter and invalid value
:type parameter: tuple(str or unicode, int)
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
name, value = parameter
config[name] = value
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_file_not_found(tmp_file, parameter):
"""
Test that providing a missing file for a file parameter returns a
non-zero exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
:param parameter: Parameter
:type parameter: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[parameter] = "foo"
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_build_indices_false_no_such_index_dir(tmpdir):
"""
Test that :py:const:`riboviz.params.BUILD_INDICES` is false
and no such index directory :py:const:`riboviz.params.INDEX_DIR`
returns a non-zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.BUILD_INDICES] = False
config[params.INDEX_DIR] = "NoSuchDirectory"
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_max_read_length_less_min(tmpdir):
"""
Test that :py:const:`riboviz.params.MAX_READ_LENGTH` less than
:py:const:`riboviz.params.MIN_READ_LENGTH` returns a non-zero exit
code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.MIN_READ_LENGTH] = 10
config[params.MAX_READ_LENGTH] = 9
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_file_not_found(tmpdir, parameter):
"""
Test that providing a missing file for a file parameter returns a
non-zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
:param parameter: Parameter
:type parameter: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[parameter] = "foo"
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_no_sample_multiplex_fq_files(tmpdir):
"""
Test that missing :py:const:`riboviz.params.FQ_FILES` and
:py:const:`riboviz.params.MULTIPLEX_FQ_FILES` returns a non-zero
exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.FQ_FILES] = []
config[params.MULTIPLEX_FQ_FILES] = []
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_invalid_value(tmp_file, parameter):
"""
Test that providing invalid values for a parameter returns a
non-zero exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
:param parameter: Parameter and invalid value
:type parameter: tuple(str or unicode, int)
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
name, value = parameter
config[name] = value
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_t_rna_codon_positions_either_or(tmpdir, parameter):
"""
Test that validating a configuration with co-dependent optional
file parameters - t_rna_file and codon_positions_file - where
one is defined and the other is not.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
:param parameter: Parameter
:type parameter: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[parameter] = None
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_t_rna_codon_positions_none(tmpdir):
"""
Test that validating a configuration with optional file
parameters t_rna_file and codon_positions_file set to
'none' returns a zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.T_RNA_FILE] = None
config[params.CODON_POSITIONS_FILE] = None
config[params.VALIDATE_ONLY] = True
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code == 0, \
"Unexpected exit code %d" % exit_code
def test_validate_skip_inputs_multiplex_fq_files_not_found(tmp_file):
"""
Test that non-existent
:py:const:`riboviz.params.MULTIPLEX_FQ_FILES` in the presence of
both :py:const:`riboviz.params.VALIDATE_ONLY` and
:py:const:`riboviz.params.SKIP_INPUTS` returns a zero exit code.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
"""
with open(riboviz.test.SIMDATA_MULTIPLEX_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.MULTIPLEX_FQ_FILES] = ["foo1.fq", "foo2.fq"]
config[params.VALIDATE_ONLY] = True
config[params.SKIP_INPUTS] = True
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code == 0, \
"Unexpected exit code %d" % exit_code
def test_optional_file_none(tmpdir, parameter):
"""
Test that validating a configuration with optional file parameters
set to 'none' returns a zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
:param parameter: Parameter
:type parameter: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[parameter] = None
config[params.VALIDATE_ONLY] = True
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code == 0, \
"Unexpected exit code %d" % exit_code
def test_validate_skip_inputs_dir_in_not_found(tmpdir):
"""
Test that a non-existent :py:const:`riboviz.params.INPUT_DIR`
directory #in the presence of both
:py:const:`riboviz.params.VALIDATE_ONLY` and
:py:const:`riboviz.params.SKIP_INPUTS` returns a zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.INPUT_DIR] = "foo"
config[params.VALIDATE_ONLY] = True
config[params.SKIP_INPUTS] = True
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code == 0, \
"Unexpected exit code %d" % exit_code
def test_validate_skip_inputs_multiplex_fq_files_not_found(tmpdir):
"""
Test that non-existent
:py:const:`riboviz.params.MULTIPLEX_FQ_FILES` in the presence of
both :py:const:`riboviz.params.VALIDATE_ONLY` and
:py:const:`riboviz.params.SKIP_INPUTS` returns a zero exit code.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
"""
with open(riboviz.test.SIMDATA_MULTIPLEX_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
config[params.MULTIPLEX_FQ_FILES] = ["foo1.fq", "foo2.fq"]
config[params.VALIDATE_ONLY] = True
config[params.SKIP_INPUTS] = True
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code == 0, \
"Unexpected exit code %d" % exit_code
def test_no_mandatory_parameter(tmp_file, parameter):
"""
Test that not providing a mandatory parameter returns a non-zero
exit code.
This test also covers the case where if one of
:py:const:`riboviz.params.T_RNA_FILE` or
:py:const:`riboviz.params.CODON_POSITIONS_FILE` is provided then
then the other must be too.
:param tmp_file: Path to temporary file, to write configuration to
:type tmp_file: str or unicode
:param parameter: Parameter
:type parameter: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
del config[parameter]
with open(tmp_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(tmp_file)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
def test_no_mandatory_parameter(tmpdir, parameter):
"""
Test that not providing a mandatory parameter returns a non-zero
exit code.
This test also covers the case where if one of
:py:const:`riboviz.params.T_RNA_FILE` or
:py:const:`riboviz.params.CODON_POSITIONS_FILE` is provided then
then the other must be too.
:param tmpdir: Temporary directory (pytest built-in fixture)
:type tmpdir: py._path.local.LocalPath
:param parameter: Parameter
:type parameter: str or unicode
"""
with open(riboviz.test.VIGNETTE_CONFIG, 'r') as f:
config = yaml.load(f, yaml.SafeLoader)
del config[parameter]
config_file = tmpdir.join("config.yaml")
with open(config_file, 'w') as f:
yaml.dump(config, f)
exit_code = run_nextflow(config_file, validate_only=True)
assert exit_code != 0, \
"Unexpected exit code %d" % exit_code
