def test_complete_intersection_with_exclusion(
self, samples):
""" Comprehensive exclusion can leave no Samples. """
prj = mock.MagicMock(samples=samples)
observed = fetch_samples(
prj, selector_attribute="protocol", selector_exclude=list(BASIC_PROTOCOL_NAMES))
_assert_samples([], observed)
def test_complete_intersection_with_exclusion(
self, samples):
""" Comprehensive exclusion can leave no Samples. """
prj = mock.MagicMock(samples=samples)
observed = fetch_samples(
prj, selector_attribute="protocol", selector_exclude=list(BASIC_PROTOCOL_NAMES))
_assert_samples([], observed)
def test_empty_intersection_with_inclusion(
self, samples, selector_attribute, selector_include):
""" Sensitivity and specificity for positive protocol selection. """
prj = mock.MagicMock(samples=samples)
observed = fetch_samples(
prj, selector_attribute=selector_attribute, selector_include=selector_include)
assert set() == set(observed)
def test_empty_intersection_with_inclusion(
self, samples, selector_attribute, selector_include):
""" Sensitivity and specificity for positive protocol selection. """
prj = mock.MagicMock(samples=samples)
observed = fetch_samples(
prj, selector_attribute=selector_attribute, selector_include=selector_include)
assert set() == set(observed)
def test_empty_intersection_with_exclusion(
self, samples, selector_attribute, selector_exclude):
""" Empty intersection with selector_exclude means all Samples remain. """
prj = mock.MagicMock(samples=samples)
expected = {s.name for s in samples}
observed = fetch_samples(prj,
selector_attribute=selector_attribute, selector_exclude=selector_exclude)
_assert_samples(expected, observed)
def test_empty_intersection_with_exclusion(
self, samples, selector_attribute, selector_exclude):
""" Empty intersection with selector_exclude means all Samples remain. """
prj = mock.MagicMock(samples=samples)
expected = {s.name for s in samples}
observed = fetch_samples(prj,
selector_attribute=selector_attribute, selector_exclude=selector_exclude)
_assert_samples(expected, observed)
def test_complete_intersection_with_inclusion(
self, samples):
""" Project with Sample set a subset of selector_include has all fetched. """
prj = mock.MagicMock(samples=samples)
expected = {s.name for s in samples}
inclusion_protocols = list(BASIC_PROTOCOL_NAMES)
print("Inclusion protocols: {}".format(inclusion_protocols))
observed = fetch_samples(prj, selector_include=inclusion_protocols)
_assert_samples(expected, observed)
def test_complete_intersection_with_inclusion(
self, samples):
""" Project with Sample set a subset of selector_include has all fetched. """
prj = mock.MagicMock(samples=samples)
expected = {s.name for s in samples}
inclusion_protocols = list(BASIC_PROTOCOL_NAMES)
print("Inclusion protocols: {}".format(inclusion_protocols))
observed = fetch_samples(prj, selector_include=inclusion_protocols)
_assert_samples(expected, observed)
def test_partial_intersection_with_exclusion(
self, samples, selector_attribute, selector_exclude, expected_sample_names):
""" Sensitivity and specificity for negative protocol selection. """
# Mock out the Project instance.
prj = mock.MagicMock(samples=samples)
# Make the call and the relevant assertions.
observed = fetch_samples(prj,
selector_attribute=selector_attribute, selector_exclude=selector_exclude)
print(expected_sample_names)
print(observed)
_assert_samples(expected_sample_names, observed)
def test_partial_intersection_with_exclusion(
self, samples, selector_attribute, selector_exclude, expected_sample_names):
""" Sensitivity and specificity for negative protocol selection. """
# Mock out the Project instance.
prj = mock.MagicMock(samples=samples)
# Make the call and the relevant assertions.
observed = fetch_samples(prj,
selector_attribute=selector_attribute, selector_exclude=selector_exclude)
print(expected_sample_names)
print(observed)
_assert_samples(expected_sample_names, observed)
def test_partial_intersection_with_inclusion(self,
samples, selector_attribute, selector_include, expected_sample_names):
""" Empty intersection with the selector_include means no Samples. """
# Mock the Project instance.
prj = mock.MagicMock(samples=samples)
# Debug aid (only visible if failed)
print("Grouped sample names (by protocol): {}".
format(_group_samples_by_protocol()))
print("Inclusion specification: {}".format(selector_include))
# Perform the call under test and make the associated assertions.
observed = fetch_samples(
prj, selector_attribute=selector_attribute, selector_include=selector_include)
_assert_samples(expected_sample_names, observed)
def test_partial_intersection_with_inclusion(self,
samples, selector_attribute, selector_include, expected_sample_names):
""" Empty intersection with the selector_include means no Samples. """
# Mock the Project instance.
prj = mock.MagicMock(samples=samples)
# Debug aid (only visible if failed)
print("Grouped sample names (by protocol): {}".
format(_group_samples_by_protocol()))
print("Inclusion specification: {}".format(selector_include))
# Perform the call under test and make the associated assertions.
observed = fetch_samples(
prj, selector_attribute=selector_attribute, selector_include=selector_include)
_assert_samples(expected_sample_names, observed)
def test_samples_without_protocol_are_not_included(
self, samples, selector_attribute, selector_include, expected_names):
""" Inclusion does not grab Sample lacking protocol. """
# Note that the expectations fixture isn't used here since this does
# not fit the generic framework in which that one applies.
prj = mock.MagicMock(samples=samples)
# Remove protocol for ATAC-Seq samples.
for s in samples:
if s[ASSAY_KEY] == "ATAC-Seq":
del s[ASSAY_KEY]
observed = fetch_samples(
prj, selector_attribute=selector_attribute, selector_include=selector_include)
_assert_samples(expected_names, observed)
def test_samples_without_protocol_are_not_included(
self, samples, selector_attribute, selector_include, expected_names):
""" Inclusion does not grab Sample lacking protocol. """
# Note that the expectations fixture isn't used here since this does
# not fit the generic framework in which that one applies.
prj = mock.MagicMock(samples=samples)
# Remove protocol for ATAC-Seq samples.
for s in samples:
if s.protocol == "ATAC-Seq":
delattr(s, "protocol")
observed = fetch_samples(
prj, selector_attribute=selector_attribute, selector_include=selector_include)
_assert_samples(expected_names, observed)
def test_equivalence_with_subproject(
self, tmpdir, samples, selector_attribute, selector_include):
""" Selection for protocol(s) is like specific subproject. """
sp_name = "atac"
confpath = _write_project_files(
tmpdir, all_samples=samples, sp_name=sp_name,
sp_samples=list(filter(lambda s: s.protocol in selector_include, samples)))
try:
full_project = Project(confpath)
except Exception:
anns_file = os.path.join(tmpdir.strpath, METADATA_KEY, "anns.csv")
print("Annotations file lines:")
with open(anns_file, 'r') as f:
print(f.readlines())
raise
subproject = Project(confpath, subproject=sp_name)
expected = {s.name for s in subproject.samples}
observed = fetch_samples(full_project,
selector_attribute=selector_attribute, selector_include=selector_include)
_assert_samples(expected, observed_samples=observed)
def test_equivalence_with_subproject(
self, tmpdir, samples, selector_attribute, selector_include):
""" Selection for protocol(s) is like specific subproject. """
sp_name = "atac"
confpath = _write_project_files(
tmpdir, all_samples=samples, sp_name=sp_name,
sp_samples=list(filter(lambda s: s.protocol in selector_include, samples)))
try:
full_project = Project(confpath)
except Exception:
anns_file = os.path.join(tmpdir.strpath, METADATA_KEY, "anns.csv")
print("Annotations file lines:")
with open(anns_file, 'r') as f:
print(f.readlines())
raise
subproject = Project(confpath, subproject=sp_name)
expected = {s.name for s in subproject.samples}
observed = fetch_samples(full_project,
selector_attribute=selector_attribute, selector_include=selector_include)
_assert_samples(expected, observed_samples=observed)
def test_samples_without_protocol_are_not_excluded(
self, samples, spare_via_anonymity):
""" Negative selection on protocol leaves Samples without protocol. """
# Strategy: specify all of the protocols as exclusions, then allow
# the parameterization to specify which are to be "spared" exclusion
# by removing the protocol selector_attribute
print("Spare input: {}".format(spare_via_anonymity))
# Account for varied argument types, and contextualize the protocol
# names with the test case parameterization. That is, vary them as they
# were in the creation of the value supplied via the samples fixture.
if isinstance(spare_via_anonymity, str):
spare_via_anonymity = [spare_via_anonymity]
spare_via_anonymity = list(spare_via_anonymity)
print("Modified spare: {}".format(spare_via_anonymity))
# Remove the protocols designated for sparing (from selector_exclude).
for s in samples:
if s.protocol in spare_via_anonymity:
delattr(s, "protocol")
print("Protocols on samples: {}".format(
{s.protocol for s in samples if hasattr(s, "protocol")}))
print("Protocols to spare: {}".format(spare_via_anonymity))
print("Non-protocol Samples: {}".format(
{s.name for s in samples if not hasattr(s, "protocol")}))
# Mock out the project with the updated Sample objects.
prj = mock.MagicMock(samples=samples)
# Expected names are associated with protocols spared selector_exclude.
sample_names_by_protocol = _group_samples_by_protocol()
expected_names = set(itertools.chain.from_iterable(
sample_names_by_protocol[p] for p in spare_via_anonymity))
# Make the call and relevant assertions.
observed = fetch_samples(
prj, selector_attribute="protocol", selector_exclude=list(BASIC_PROTOCOL_NAMES))
_assert_samples(expected_names, observed)
def test_samples_without_protocol_are_not_excluded(
self, samples, spare_via_anonymity):
""" Negative selection on protocol leaves Samples without protocol. """
# Strategy: specify all of the protocols as exclusions, then allow
# the parameterization to specify which are to be "spared" exclusion
# by removing the protocol selector_attribute
print("Spare input: {}".format(spare_via_anonymity))
# Account for varied argument types, and contextualize the protocol
# names with the test case parameterization. That is, vary them as they
# were in the creation of the value supplied via the samples fixture.
if isinstance(spare_via_anonymity, str):
spare_via_anonymity = [spare_via_anonymity]
spare_via_anonymity = list(spare_via_anonymity)
print("Modified spare: {}".format(spare_via_anonymity))
# Remove the protocols designated for sparing (from selector_exclude).
for s in samples:
if s[ASSAY_KEY] in spare_via_anonymity:
del s[ASSAY_KEY]
print("Protocols on samples: {}".format(
{s.protocol for s in samples if hasattr(s, "protocol")}))
print("Protocols to spare: {}".format(spare_via_anonymity))
print("Non-protocol Samples: {}".format(
{s.name for s in samples if not hasattr(s, "protocol")}))
# Mock out the project with the updated Sample objects.
prj = mock.MagicMock(samples=samples)
# Expected names are associated with protocols spared selector_exclude.
sample_names_by_protocol = _group_samples_by_protocol()
expected_names = set(itertools.chain.from_iterable(
sample_names_by_protocol[p] for p in spare_via_anonymity))
# Make the call and relevant assertions.
observed = fetch_samples(
prj, selector_attribute="protocol", selector_exclude=list(BASIC_PROTOCOL_NAMES))
_assert_samples(expected_names, observed)
def test_no_samples(selector_attribute, selector_include, selector_exclude):
""" Regardless of filtration, lack of samples means empty collection. """
prj = mock.MagicMock(samples=[])
observed = fetch_samples(prj, selector_attribute=selector_attribute,
selector_include=selector_include, selector_exclude=selector_exclude)
assert [] == observed
def test_no_filter(selector_attribute, selector_include, selector_exclude, samples):
""" Without a filtration mechanism, all Samples are retained. """
prj = mock.MagicMock(samples=samples)
assert samples == fetch_samples(prj, selector_attribute=selector_attribute,
selector_include=selector_include, selector_exclude=selector_exclude)
def test_only_inclusion_or_exclusion(selector_attribute, selector_include, selector_exclude, samples):
""" Only an selector_include or selector_exclude set is permitted. """
prj = mock.MagicMock(samples=samples)
with pytest.raises(TypeError):
fetch_samples(prj, selector_attribute,
selector_include=selector_include, selector_exclude=selector_exclude)
def test_only_inclusion_or_exclusion(selector_attribute, selector_include, selector_exclude, samples):
""" Only an selector_include or selector_exclude set is permitted. """
prj = mock.MagicMock(samples=samples)
with pytest.raises(TypeError):
fetch_samples(prj, selector_attribute,
selector_include=selector_include, selector_exclude=selector_exclude)
def test_no_samples(selector_attribute, selector_include, selector_exclude):
""" Regardless of filtration, lack of samples means empty collection. """
prj = mock.MagicMock(samples=[])
observed = fetch_samples(prj, selector_attribute=selector_attribute,
selector_include=selector_include, selector_exclude=selector_exclude)
assert [] == observed
def test_no_filter(selector_attribute, selector_include, selector_exclude, samples):
""" Without a filtration mechanism, all Samples are retained. """
prj = mock.MagicMock(samples=samples)
assert samples == fetch_samples(prj, selector_attribute=selector_attribute,
selector_include=selector_include, selector_exclude=selector_exclude)
def test_has_attribute(selector_attribute, selector_exclude, samples):
""" At least one of the samples has to have the specified selector_attribute. """
prj = mock.MagicMock(samples=samples)
with pytest.raises(AttributeError):
fetch_samples(prj, selector_attribute=selector_attribute, selector_exclude=selector_exclude)
def test_has_attribute(selector_attribute, selector_exclude, samples):
""" At least one of the samples has to have the specified selector_attribute. """
prj = mock.MagicMock(samples=samples)
with pytest.raises(AttributeError):
fetch_samples(prj, selector_attribute=selector_attribute, selector_exclude=selector_exclude)