def test_full_multi_analysis(self):
analysis = self.create_analysis(
FullMultiAnalysis,
'full', [
FilesetFilter('a', 'ones', text_format),
FilesetFilter('b', 'ones', text_format),
FilesetFilter('c', 'ones', text_format)
],
parameters=[Parameter('required_op', 'mul')])
d, e, f = analysis.data(('d', 'e', 'f'),
derive=True,
subject_id='SUBJECT',
visit_id='VISIT')
self.assertContentsEqual(d, 2.0)
self.assertContentsEqual(e, 3.0)
self.assertContentsEqual(f, 6.0)
# Test parameter values in MultiAnalysis
self.assertEqual(analysis._get_parameter('p1').value, 100)
self.assertEqual(analysis._get_parameter('p2').value, '200')
self.assertEqual(analysis._get_parameter('p3').value, 300.0)
self.assertEqual(analysis._get_parameter('q1').value, 150)
self.assertEqual(analysis._get_parameter('q2').value, '250')
self.assertEqual(analysis._get_parameter('required_op').value, 'mul')
# Test parameter values in SubComp
ss1 = analysis.subcomp('ss1')
self.assertEqual(ss1._get_parameter('o1').value, 100)
self.assertEqual(ss1._get_parameter('o2').value, '200')
self.assertEqual(ss1._get_parameter('o3').value, 300.0)
ss2 = analysis.subcomp('ss2')
self.assertEqual(ss2._get_parameter('o1').value, 150)
self.assertEqual(ss2._get_parameter('o2').value, '250')
self.assertEqual(ss2._get_parameter('o3').value, 300.0)
self.assertEqual(ss2._get_parameter('product_op').value, 'mul')
def test_partial_multi_analysis(self):
analysis = self.create_analysis(
PartialMultiAnalysis,
'partial', [
FilesetFilter('a', 'ones', text_format),
FilesetFilter('b', 'ones', text_format),
FilesetFilter('c', 'ones', text_format)
],
parameters=[Parameter('ss2_product_op', 'mul')])
ss1_z = analysis.data('ss1_z',
subject_id='SUBJECT',
visit_id='VISIT',
derive=True)
ss2_z = list(analysis.data('ss2_z', derive=True))[0]
self.assertContentsEqual(ss1_z, 2.0)
self.assertContentsEqual(analysis.data('ss2_y', derive=True), 3.0)
self.assertContentsEqual(ss2_z, 6.0)
# Test parameter values in MultiAnalysis
self.assertEqual(analysis._get_parameter('p1').value, 1000)
self.assertEqual(analysis._get_parameter('ss1_o2').value, '2')
self.assertEqual(analysis._get_parameter('ss1_o3').value, 3.0)
self.assertEqual(analysis._get_parameter('ss2_o2').value, '20')
self.assertEqual(analysis._get_parameter('ss2_o3').value, 30.0)
self.assertEqual(
analysis._get_parameter('ss2_product_op').value, 'mul')
# Test parameter values in SubComp
ss1 = analysis.subcomp('ss1')
self.assertEqual(ss1._get_parameter('o1').value, 1000)
self.assertEqual(ss1._get_parameter('o2').value, '2')
self.assertEqual(ss1._get_parameter('o3').value, 3.0)
ss2 = analysis.subcomp('ss2')
self.assertEqual(ss2._get_parameter('o1').value, 1000)
self.assertEqual(ss2._get_parameter('o2').value, '20')
self.assertEqual(ss2._get_parameter('o3').value, 30.0)
self.assertEqual(ss2._get_parameter('product_op').value, 'mul')
def test_multi_analysis_generated_cls_pickle(self):
cls_dct = {
'add_subcomp_specs': [
SubCompSpec('ss1', BasicTestAnalysis),
SubCompSpec('ss2', BasicTestAnalysis)
]
}
MultiGeneratedClass = MultiAnalysisMetaClass('MultiGeneratedClass',
(MultiAnalysis, ),
cls_dct)
analysis = self.create_analysis(
MultiGeneratedClass,
'multi_gen_cls',
inputs=[
FilesetFilter('ss1_fileset', 'fileset', text_format),
FilesetFilter('ss2_fileset', 'fileset', text_format)
])
pkl_path = os.path.join(self.work_dir, 'multi_gen_cls.pkl')
with open(pkl_path, 'wb') as f:
pkl.dump(analysis, f)
del MultiGeneratedClass
with open(pkl_path, 'rb') as f:
regen = pkl.load(f)
self.assertContentsEqual(regen.data('ss2_out_fileset', derive=True),
'foo')
def test_input_validation_fail(self):
self.assertRaises(ArcanaUsageError,
self.create_analysis,
TestInputValidationAnalysis,
'test_validation_fail',
inputs=[
FilesetFilter('a', 'a', test3_format),
FilesetFilter('b', 'b', test3_format)
])
def test_input_validation(self):
self.create_analysis(TestInputValidationAnalysis,
'test_input_validation',
inputs=[
FilesetFilter('a', 'a', test1_format),
FilesetFilter('b', 'b', test3_format),
FilesetFilter('c', 'a', test1_format),
FilesetFilter('d', 'd', test3_format)
])
def make_analysis(self):
return self.create_analysis(ExampleAnalysis,
'dummy',
inputs=[
FilesetFilter('one', 'one_input',
text_format),
FilesetFilter('ten', 'ten_input',
text_format)
],
parameters={'pipeline_parameter': True})
def test_repository_roundtrip(self):
analysis = DummyAnalysis(self.STUDY_NAME,
self.dataset,
processor=SingleProc('a_dir'),
inputs=[
FilesetFilter('source1', 'source1',
text_format),
FilesetFilter('source2', 'source2',
text_format),
FilesetFilter('source3', 'source3',
text_format),
FilesetFilter('source4', 'source4',
text_format)
])
# TODO: Should test out other file formats as well.
source_files = ('source1', 'source2', 'source3', 'source4')
sink_files = ('sink1', 'sink3', 'sink4')
inputnode = pe.Node(IdentityInterface(['subject_id', 'visit_id']),
'inputnode')
inputnode.inputs.subject_id = self.SUBJECT
inputnode.inputs.visit_id = self.VISIT
source = pe.Node(RepositorySource(
analysis.bound_spec(f).slice for f in source_files),
name='source')
dummy_pipeline = analysis.dummy_pipeline()
dummy_pipeline.cap()
sink = pe.Node(RepositorySink((analysis.bound_spec(f).slice
for f in sink_files), dummy_pipeline),
name='sink')
sink.inputs.name = 'repository_sink'
sink.inputs.desc = (
"A test session created by repository roundtrip unittest")
# Create workflow connecting them together
workflow = pe.Workflow('source_sink_unit_test', base_dir=self.work_dir)
workflow.add_nodes((source, sink))
workflow.connect(inputnode, 'subject_id', source, 'subject_id')
workflow.connect(inputnode, 'visit_id', source, 'visit_id')
workflow.connect(inputnode, 'subject_id', sink, 'subject_id')
workflow.connect(inputnode, 'visit_id', sink, 'visit_id')
for source_name in source_files:
if not source_name.endswith('2'):
sink_name = source_name.replace('source', 'sink')
workflow.connect(source, source_name + PATH_SUFFIX, sink,
sink_name + PATH_SUFFIX)
workflow.run()
# Check local directory was created properly
outputs = [
f for f in sorted(
os.listdir(self.get_session_dir(
from_analysis=self.STUDY_NAME)))
if f not in (LocalFileSystemRepo.FIELDS_FNAME,
LocalFileSystemRepo.PROV_DIR)
]
self.assertEqual(outputs, ['sink1.txt', 'sink3.txt', 'sink4.txt'])
def test_format_conversions(self):
analysis = self.create_analysis(
ConversionAnalysis, 'conversion', [
FilesetFilter('text', 'text', text_format),
FilesetFilter('directory', 'directory', directory_format),
FilesetFilter('zip', 'zip', zip_format)])
self.assertCreated(list(analysis.data('text_from_text', derive=True))[0])
self.assertCreated(list(analysis.data('directory_from_zip_on_input', derive=True))[0])
self.assertCreated(list(analysis.data('zip_from_directory_on_input', derive=True))[0])
self.assertCreated(list(analysis.data('directory_from_zip_on_output', derive=True))[0])
self.assertCreated(list(analysis.data('zip_from_directory_on_output', derive=True))[0])
def test_derivable(self):
# Test vanilla analysis
analysis = self.create_analysis(
TestDerivableAnalysis,
'analysis',
inputs={'required': 'required'})
self.assertTrue(analysis.spec('derivable').derivable)
self.assertTrue(
analysis.spec('another_derivable').derivable)
self.assertFalse(
analysis.spec('missing_input').derivable)
self.assertFalse(
analysis.spec('requires_switch').derivable)
self.assertFalse(
analysis.spec('requires_switch2').derivable)
self.assertTrue(analysis.spec('requires_foo').derivable)
self.assertFalse(analysis.spec('requires_bar').derivable)
# Test analysis with 'switch' enabled
analysis_with_switch = self.create_analysis(
TestDerivableAnalysis,
'analysis_with_switch',
inputs=[FilesetFilter('required', 'required', text_format)],
parameters={'switch': True})
self.assertTrue(
analysis_with_switch.spec('requires_switch').derivable)
self.assertTrue(
analysis_with_switch.spec('requires_switch2').derivable)
# Test analysis with branch=='bar'
analysis_bar_branch = self.create_analysis(
TestDerivableAnalysis,
'analysis_bar_branch',
inputs=[FilesetFilter('required', 'required', text_format)],
parameters={'branch': 'bar'})
self.assertFalse(analysis_bar_branch.spec('requires_foo').derivable)
self.assertTrue(analysis_bar_branch.spec('requires_bar').derivable)
# Test analysis with optional input
analysis_with_input = self.create_analysis(
TestDerivableAnalysis,
'analysis_with_inputs',
inputs=[FilesetFilter('required', 'required', text_format),
FilesetFilter('optional', 'required', text_format)])
self.assertTrue(
analysis_with_input.spec('missing_input').derivable)
analysis_unhandled = self.create_analysis(
TestDerivableAnalysis,
'analysis_unhandled',
inputs=[FilesetFilter('required', 'required', text_format)],
parameters={'branch': 'wee'})
self.assertRaises(
ArcanaDesignError,
getattr,
analysis_unhandled.spec('requires_foo'),
'derivable')
def test_order_match(self):
analysis = self.create_analysis(
TestMatchAnalysis, 'test_dicom',
inputs=[
FilesetFilter('gre_phase', pattern=self.GRE_PATTERN,
valid_formats=dicom_format, order=1,
is_regex=True),
FilesetFilter('gre_mag', pattern=self.GRE_PATTERN,
valid_formats=dicom_format, order=0,
is_regex=True)])
phase = list(analysis.data('gre_phase', derive=True))[0]
mag = list(analysis.data('gre_mag', derive=True))[0]
self.assertEqual(phase.name, 'gre_field_mapping_3mm_phase')
self.assertEqual(mag.name, 'gre_field_mapping_3mm_mag')
def test_id_match(self):
analysis = test_data.TestMatchAnalysis(
name='test_dicom',
dataset=XnatRepo(server=SERVER,
cache_dir=tempfile.mkdtemp()).dataset(
self.project),
processor=SingleProc(self.work_dir),
inputs=[
FilesetFilter('gre_phase', valid_formats=dicom_format, id=7),
FilesetFilter('gre_mag', valid_formats=dicom_format, id=6)
])
phase = list(analysis.data('gre_phase', derive=True))[0]
mag = list(analysis.data('gre_mag', derive=True))[0]
self.assertEqual(phase.name, 'gre_field_mapping_3mm_phase')
self.assertEqual(mag.name, 'gre_field_mapping_3mm_mag')
def test_per_session_prereqs(self):
# Generate all data for 'thousand' spec
analysis = self.create_analysis(
ExistingPrereqAnalysis,
self.STUDY_NAME,
inputs=[FilesetFilter('one', 'one', text_format)])
analysis.derive('thousand')
targets = {
'subject1': {
'visit1': 1100.0,
'visit2': 1110.0,
'visit3': 1000.0
},
'subject2': {
'visit1': 1111.0,
'visit2': 1110.0,
'visit3': 1000.0
}
}
tree = self.dataset.tree
for subj_id, visits in self.PROJECT_STRUCTURE.items():
for visit_id in visits:
session = tree.subject(subj_id).session(visit_id)
fileset = session.fileset('thousand',
from_analysis=self.STUDY_NAME)
fileset.format = text_format
self.assertContentsEqual(fileset, targets[subj_id][visit_id],
"{}:{}".format(subj_id, visit_id))
def test_fields_roundtrip(self):
repository = XnatRepo(server=SERVER, cache_dir=self.cache_dir)
dataset = repository.dataset(self.project)
analysis = DummyAnalysis(
self.STUDY_NAME,
dataset=dataset,
processor=SingleProc('a_dir'),
inputs=[FilesetFilter('source1', 'source1', text_format)])
fields = ['field{}'.format(i) for i in range(1, 4)]
dummy_pipeline = analysis.dummy_pipeline()
dummy_pipeline.cap()
sink = pe.Node(RepositorySink(
(analysis.bound_spec(f).slice for f in fields), dummy_pipeline),
name='fields_sink')
sink.inputs.field1_field = field1 = 1
sink.inputs.field2_field = field2 = 2.0
sink.inputs.field3_field = field3 = str('3')
sink.inputs.subject_id = self.SUBJECT
sink.inputs.visit_id = self.VISIT
sink.inputs.desc = "Test sink of fields"
sink.inputs.name = 'test_sink'
sink.run()
source = pe.Node(RepositorySource(
analysis.bound_spec(f).slice for f in fields),
name='fields_source')
source.inputs.visit_id = self.VISIT
source.inputs.subject_id = self.SUBJECT
source.inputs.desc = "Test source of fields"
source.inputs.name = 'test_source'
results = source.run()
self.assertEqual(results.outputs.field1_field, field1)
self.assertEqual(results.outputs.field2_field, field2)
self.assertEqual(results.outputs.field3_field, field3)
def test_multi_multi_analysis(self):
analysis = self.create_analysis(
MultiMultiAnalysis,
'multi_multi', [
FilesetFilter('ss1_x', 'ones', text_format),
FilesetFilter('ss1_y', 'ones', text_format),
FilesetFilter('full_a', 'ones', text_format),
FilesetFilter('full_b', 'ones', text_format),
FilesetFilter('full_c', 'ones', text_format),
FilesetFilter('partial_a', 'ones', text_format),
FilesetFilter('partial_b', 'ones', text_format),
FilesetFilter('partial_c', 'ones', text_format)
],
parameters=[
Parameter('full_required_op', 'mul'),
Parameter('partial_ss2_product_op', 'mul')
])
self.assertContentsEqual(analysis.data('g', derive=True), 11.0)
# Test parameter values in MultiAnalysis
self.assertEqual(analysis._get_parameter('full_p1').value, 100)
self.assertEqual(analysis._get_parameter('full_p2').value, '200')
self.assertEqual(analysis._get_parameter('full_p3').value, 300.0)
self.assertEqual(analysis._get_parameter('full_q1').value, 150)
self.assertEqual(analysis._get_parameter('full_q2').value, '250')
self.assertEqual(
analysis._get_parameter('full_required_op').value, 'mul')
# Test parameter values in SubComp
ss1 = analysis.subcomp('full').subcomp('ss1')
self.assertEqual(ss1._get_parameter('o1').value, 100)
self.assertEqual(ss1._get_parameter('o2').value, '200')
self.assertEqual(ss1._get_parameter('o3').value, 300.0)
ss2 = analysis.subcomp('full').subcomp('ss2')
self.assertEqual(ss2._get_parameter('o1').value, 150)
self.assertEqual(ss2._get_parameter('o2').value, '250')
self.assertEqual(ss2._get_parameter('o3').value, 300.0)
self.assertEqual(ss2._get_parameter('product_op').value, 'mul')
# Test parameter values in MultiAnalysis
self.assertEqual(analysis._get_parameter('partial_p1').value, 1000)
self.assertEqual(analysis._get_parameter('partial_ss1_o2').value, '2')
self.assertEqual(analysis._get_parameter('partial_ss1_o3').value, 3.0)
self.assertEqual(analysis._get_parameter('partial_ss2_o2').value, '20')
self.assertEqual(analysis._get_parameter('partial_ss2_o3').value, 30.0)
self.assertEqual(
analysis._get_parameter('partial_ss2_product_op').value, 'mul')
# Test parameter values in SubComp
ss1 = analysis.subcomp('partial').subcomp('ss1')
self.assertEqual(ss1._get_parameter('o1').value, 1000)
self.assertEqual(ss1._get_parameter('o2').value, '2')
self.assertEqual(ss1._get_parameter('o3').value, 3.0)
ss2 = analysis.subcomp('partial').subcomp('ss2')
self.assertEqual(ss2._get_parameter('o1').value, 1000)
self.assertEqual(ss2._get_parameter('o2').value, '20')
self.assertEqual(ss2._get_parameter('o3').value, 30.0)
self.assertEqual(ss2._get_parameter('product_op').value, 'mul')
def test_scan_label_quality(self):
tmp_dir = tempfile.mkdtemp()
repository = XnatRepo(server=SERVER, cache_dir=tmp_dir)
dataset = repository.dataset(self.project,
subject_ids=[self.SUBJECT],
visit_ids=[self.VISIT])
tree = dataset.tree
for accepted, expected in ((None, '1unusable'), ((None, 'questionable',
'usable'),
'2unlabelled'),
(('questionable', 'usable'),
'3questionable'), ('usable', '4usable')):
inpt = FilesetFilter('dummy',
order=0,
valid_formats=text_format,
acceptable_quality=accepted)
matched = inpt.match(tree).item(subject_id=self.SUBJECT,
visit_id=self.VISIT)
self.assertEqual(matched.name, expected)
def test_module_load_in_map(self):
analysis = self.create_analysis(
RequirementsAnalysis,
'requirements', [FilesetFilter('ones', 'ones', text_format)],
environment=ModulesEnv())
threes = analysis.data('threes', derive=True)
fours = analysis.data('fours', derive=True)
self.assertEqual(next(iter(threes)).value, 3)
self.assertEqual(next(iter(fours)).value, 4)
self.assertEqual(ModulesEnv.loaded(), {})
def test_dcm2niix(self):
analysis = self.create_analysis(
DummyAnalysis,
'concatenate',
environment=TEST_ENV,
inputs=[
FilesetFilter('input_fileset',
dicom_format, 't2_tse_tra_p2_448')])
self.assertFilesetCreated(
next(iter(analysis.data('output_fileset', derive=True))))
def test_pipeline_prerequisites(self):
analysis = self.create_analysis(ConversionAnalysis, 'conversion', [
FilesetFilter('mrtrix', 'mrtrix', text_format),
FilesetFilter('nifti_gz', text_format, 'nifti_gz'),
FilesetFilter('dicom', dicom_format,
't1_mprage_sag_p2_iso_1_ADNI'),
FilesetFilter('directory', directory_format,
't1_mprage_sag_p2_iso_1_ADNI'),
FilesetFilter('zip', 'zip', zip_format)
])
self.assertFilesetCreated(
next(iter(analysis.data('nifti_gz_from_dicom', derive=True))))
self.assertFilesetCreated(
next(iter(analysis.data('mrtrix_from_nifti_gz', derive=True))))
self.assertFilesetCreated(
next(iter(analysis.data('nifti_from_mrtrix', derive=True))))
self.assertFilesetCreated(
next(iter(analysis.data('directory_from_zip', derive=True))))
self.assertFilesetCreated(
next(iter(analysis.data('zip_from_directory', derive=True))))
def test_raised_error(self):
analysis = self.create_analysis(
BasicTestAnalysis,
'base',
inputs=[FilesetFilter('fileset', 'fileset', text_format)])
# Disable error logs as it should always throw an error
logger = logging.getLogger('nipype.workflow')
orig_level = logger.level
logger.setLevel(50)
self.assertRaises(RuntimeError, analysis.derive, 'raise_error')
logger.setLevel(orig_level)
class TestDicomTagMatch(BaseTestCase):
IMAGE_TYPE_TAG = ('0008', '0008')
GRE_PATTERN = 'gre_field_mapping_3mm.*'
PHASE_IMAGE_TYPE = ['ORIGINAL', 'PRIMARY', 'P', 'ND']
MAG_IMAGE_TYPE = ['ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM']
DICOM_MATCH = [
FilesetFilter('gre_phase', GRE_PATTERN, dicom_format,
dicom_tags={IMAGE_TYPE_TAG: PHASE_IMAGE_TYPE},
is_regex=True),
FilesetFilter('gre_mag', GRE_PATTERN, dicom_format,
dicom_tags={IMAGE_TYPE_TAG: MAG_IMAGE_TYPE},
is_regex=True)]
INPUTS_FROM_REF_DIR = True
REF_FORMATS = [dicom_format]
def test_dicom_match(self):
analysis = self.create_analysis(
TestMatchAnalysis, 'test_dicom',
inputs=self.DICOM_MATCH)
phase = list(analysis.data('gre_phase', derive=True))[0]
mag = list(analysis.data('gre_mag', derive=True))[0]
self.assertEqual(phase.name, 'gre_field_mapping_3mm_phase')
self.assertEqual(mag.name, 'gre_field_mapping_3mm_mag')
def test_order_match(self):
analysis = self.create_analysis(
TestMatchAnalysis, 'test_dicom',
inputs=[
FilesetFilter('gre_phase', pattern=self.GRE_PATTERN,
valid_formats=dicom_format, order=1,
is_regex=True),
FilesetFilter('gre_mag', pattern=self.GRE_PATTERN,
valid_formats=dicom_format, order=0,
is_regex=True)])
phase = list(analysis.data('gre_phase', derive=True))[0]
mag = list(analysis.data('gre_mag', derive=True))[0]
self.assertEqual(phase.name, 'gre_field_mapping_3mm_phase')
self.assertEqual(mag.name, 'gre_field_mapping_3mm_mag')
def test_generated_cls_pickle(self):
GeneratedClass = AnalysisMetaClass('GeneratedClass',
(BasicTestAnalysis, ), {})
analysis = self.create_analysis(
GeneratedClass,
'gen_cls',
inputs=[FilesetFilter('fileset', 'fileset', text_format)])
pkl_path = os.path.join(self.work_dir, 'gen_cls.pkl')
with open(pkl_path, 'wb') as f:
pkl.dump(analysis, f)
del GeneratedClass
with open(pkl_path, 'rb') as f:
regen = pkl.load(f)
self.assertContentsEqual(regen.data('out_fileset', derive=True), 'foo')
def test_genenerated_method_pickle_fail(self):
cls_dct = {
'add_subcomp_specs': [
SubCompSpec('ss1', BasicTestAnalysis),
SubCompSpec('ss2', BasicTestAnalysis)
],
'default_fileset_pipeline':
MultiAnalysis.translate('ss1', 'pipeline')
}
MultiGeneratedClass = MultiAnalysisMetaClass('MultiGeneratedClass',
(MultiAnalysis, ),
cls_dct)
analysis = self.create_analysis(
MultiGeneratedClass,
'multi_gen_cls',
inputs=[
FilesetFilter('ss1_fileset', 'fileset', text_format),
FilesetFilter('ss2_fileset', 'fileset', text_format)
])
pkl_path = os.path.join(self.work_dir, 'multi_gen_cls.pkl')
with open(pkl_path, 'w') as f:
self.assertRaises(ArcanaCantPickleAnalysisError, pkl.dump,
analysis, f)
def test_cache_download(self):
repository = XnatRepo(server=SERVER, cache_dir=tempfile.mkdtemp())
dataset = repository.dataset(self.project)
analysis = self.create_analysis(
TestAnalysis,
'cache_download',
inputs=[
FilesetFilter('fileset1', 'fileset1', text_format),
FilesetFilter('fileset3', 'fileset3', text_format)
],
dataset=dataset)
analysis.cache_inputs()
for subject_id, visits in list(self.STRUCTURE.items()):
subj_dir = op.join(repository.cache_dir, self.project,
'{}_{}'.format(self.project, subject_id))
for visit_id in visits:
sess_dir = op.join(
subj_dir, '{}_{}_{}'.format(self.project, subject_id,
visit_id))
for inpt in analysis.inputs:
self.assertTrue(
op.exists(
op.join(sess_dir, inpt.name + '-' + inpt.name)))
def test_missing_parameter(self):
# Misses the required 'full_required_op' parameter, which sets
# the operation of the second node in AnalysisB's pipeline to
# 'product'
inputs = [
FilesetFilter('ss1_x', 'ones', text_format),
FilesetFilter('ss1_y', 'ones', text_format),
FilesetFilter('full_a', 'ones', text_format),
FilesetFilter('full_b', 'ones', text_format),
FilesetFilter('full_c', 'ones', text_format),
FilesetFilter('partial_a', 'ones', text_format),
FilesetFilter('partial_b', 'ones', text_format),
FilesetFilter('partial_c', 'ones', text_format)
]
missing_parameter_analysis = self.create_analysis(
MultiMultiAnalysis,
'multi_multi',
inputs,
parameters=[Parameter('partial_ss2_product_op', 'mul')])
self.assertRaises(NotSpecifiedRequiredParameter,
missing_parameter_analysis.derive, 'g')
missing_parameter_analysis2 = self.create_analysis(
MultiMultiAnalysis,
'multi_multi',
inputs,
parameters=[Parameter('full_required_op', 'mul')])
self.assertRaises(NotSpecifiedRequiredParameter,
missing_parameter_analysis2.derive, 'g')
provided_parameters_analysis = self.create_analysis(
MultiMultiAnalysis,
'multi_multi',
inputs,
parameters=[
Parameter('partial_ss2_product_op', 'mul'),
Parameter('full_required_op', 'mul')
])
g = list(provided_parameters_analysis.data('g', derive=True))[0]
self.assertContentsEqual(g, 11.0)
def add_sessions(self):
BaseMultiSubjectTestCase.add_sessions(self)
# Create a analysis object, in order to generate appropriate provenance
# for the existing "derived" data
derived_filesets = [f for f in self.DATASET_CONTENTS if f != 'one']
analysis = self.create_analysis(
ExistingPrereqAnalysis,
self.STUDY_NAME,
dataset=self.local_dataset,
inputs=[FilesetFilter('one', 'one', text_format)])
# Get all pipelines in the analysis
pipelines = {
n: getattr(analysis, '{}_pipeline'.format(n))()
for n in derived_filesets
}
for node in analysis.dataset.tree:
for fileset in node.filesets:
if fileset.basename != 'one' and fileset.exists:
# Generate expected provenance record for each pipeline
# and save in the local dataset
pipelines[fileset.name].cap()
record = pipelines[fileset.name].expected_record(node)
self.local_dataset.put_record(record)
analysis.clear_caches() # Reset dataset trees
def test_repository_roundtrip(self):
# Create working dirs
# Create DarisSource node
repository = XnatRepo(server=SERVER, cache_dir=self.cache_dir)
dataset = repository.dataset(self.project)
analysis = DummyAnalysis(self.STUDY_NAME,
dataset=dataset,
processor=SingleProc('a_dir'),
inputs=[
FilesetFilter('source1', 'source1',
text_format),
FilesetFilter('source2', 'source2',
text_format),
FilesetFilter('source3', 'source3',
text_format),
FilesetFilter('source4', 'source4',
text_format)
])
# TODO: Should test out other file formats as well.
source_files = ['source1', 'source2', 'source3', 'source4']
sink_files = ['sink1', 'sink3', 'sink4']
inputnode = pe.Node(IdentityInterface(['subject_id', 'visit_id']),
'inputnode')
inputnode.inputs.subject_id = str(self.SUBJECT)
inputnode.inputs.visit_id = str(self.VISIT)
source = pe.Node(RepositorySource(
analysis.bound_spec(f).slice for f in source_files),
name='source')
dummy_pipeline = analysis.dummy_pipeline()
dummy_pipeline.cap()
sink = pe.Node(RepositorySink((analysis.bound_spec(f).slice
for f in sink_files), dummy_pipeline),
name='sink')
sink.inputs.name = 'repository-roundtrip-unittest'
sink.inputs.desc = (
"A test session created by repository roundtrip unittest")
# Create workflow connecting them together
workflow = pe.Workflow('source-sink-unit-test', base_dir=self.work_dir)
workflow.add_nodes((source, sink))
workflow.connect(inputnode, 'subject_id', source, 'subject_id')
workflow.connect(inputnode, 'visit_id', source, 'visit_id')
workflow.connect(inputnode, 'subject_id', sink, 'subject_id')
workflow.connect(inputnode, 'visit_id', sink, 'visit_id')
for source_name in source_files:
if source_name != 'source2':
sink_name = source_name.replace('source', 'sink')
workflow.connect(source, source_name + PATH_SUFFIX, sink,
sink_name + PATH_SUFFIX)
workflow.run()
# Check cache was created properly
self.assertEqual(filter_scans(os.listdir(self.session_cache())), [
'source1-source1', 'source2-source2', 'source3-source3',
'source4-source4'
])
expected_sink_filesets = ['sink1', 'sink3', 'sink4']
self.assertEqual(
filter_scans(
os.listdir(self.session_cache(from_analysis=self.STUDY_NAME))),
[(e + '-' + e) for e in expected_sink_filesets])
with self._connect() as login:
fileset_names = filter_scans(login.experiments[self.session_label(
from_analysis=self.STUDY_NAME)].scans.keys())
self.assertEqual(fileset_names, expected_sink_filesets)
def test_summary(self):
# Create working dirs
# Create XnatSource node
repository = XnatRepo(server=SERVER, cache_dir=self.cache_dir)
analysis = DummyAnalysis(self.SUMMARY_STUDY_NAME,
repository.dataset(self.project),
SingleProc('ad'),
inputs=[
FilesetFilter('source1', 'source1',
text_format),
FilesetFilter('source2', 'source2',
text_format),
FilesetFilter('source3', 'source3',
text_format)
])
# TODO: Should test out other file formats as well.
source_files = ['source1', 'source2', 'source3']
inputnode = pe.Node(IdentityInterface(['subject_id', 'visit_id']),
'inputnode')
inputnode.inputs.subject_id = self.SUBJECT
inputnode.inputs.visit_id = self.VISIT
source = pe.Node(RepositorySource(
[analysis.bound_spec(f).slice for f in source_files]),
name='source')
subject_sink_files = ['subject_sink']
dummy_pipeline = analysis.dummy_pipeline()
dummy_pipeline.cap()
subject_sink = pe.Node(RepositorySink(
[analysis.bound_spec(f).slice for f in subject_sink_files],
dummy_pipeline),
name='subject_sink')
subject_sink.inputs.name = 'subject_summary'
subject_sink.inputs.desc = (
"Tests the sinking of subject-wide filesets")
# Test visit sink
visit_sink_files = ['visit_sink']
visit_sink = pe.Node(RepositorySink(
[analysis.bound_spec(f).slice for f in visit_sink_files],
dummy_pipeline),
name='visit_sink')
visit_sink.inputs.name = 'visit_summary'
visit_sink.inputs.desc = ("Tests the sinking of visit-wide filesets")
# Test project sink
analysis_sink_files = ['analysis_sink']
analysis_sink = pe.Node(RepositorySink(
[analysis.bound_spec(f).slice for f in analysis_sink_files],
dummy_pipeline),
name='analysis_sink')
analysis_sink.inputs.name = 'project_summary'
analysis_sink.inputs.desc = (
"Tests the sinking of project-wide filesets")
# Create workflow connecting them together
workflow = pe.Workflow('summary_unittest', base_dir=self.work_dir)
workflow.add_nodes((source, subject_sink, visit_sink, analysis_sink))
workflow.connect(inputnode, 'subject_id', source, 'subject_id')
workflow.connect(inputnode, 'visit_id', source, 'visit_id')
workflow.connect(inputnode, 'subject_id', subject_sink, 'subject_id')
workflow.connect(inputnode, 'visit_id', visit_sink, 'visit_id')
workflow.connect(source, 'source1' + PATH_SUFFIX, subject_sink,
'subject_sink' + PATH_SUFFIX)
workflow.connect(source, 'source2' + PATH_SUFFIX, visit_sink,
'visit_sink' + PATH_SUFFIX)
workflow.connect(source, 'source3' + PATH_SUFFIX, analysis_sink,
'analysis_sink' + PATH_SUFFIX)
workflow.run()
analysis.clear_caches() # Refreshed cached repository tree object
with self._connect() as login:
# Check subject summary directories were created properly in cache
expected_subj_filesets = ['subject_sink']
subject_dir = self.session_cache(
visit=XnatRepo.SUMMARY_NAME,
from_analysis=self.SUMMARY_STUDY_NAME)
self.assertEqual(filter_scans(os.listdir(subject_dir)),
[(e + '-' + e) for e in expected_subj_filesets])
# and on XNAT
subject_fileset_names = filter_scans(
login.projects[self.project].experiments[self.session_label(
visit=XnatRepo.SUMMARY_NAME,
from_analysis=self.SUMMARY_STUDY_NAME)].scans.keys())
self.assertEqual(expected_subj_filesets, subject_fileset_names)
# Check visit summary directories were created properly in
# cache
expected_visit_filesets = ['visit_sink']
visit_dir = self.session_cache(
subject=XnatRepo.SUMMARY_NAME,
from_analysis=self.SUMMARY_STUDY_NAME)
self.assertEqual(filter_scans(os.listdir(visit_dir)),
[(e + '-' + e) for e in expected_visit_filesets])
# and on XNAT
visit_fileset_names = filter_scans(
login.projects[self.project].experiments[self.session_label(
subject=XnatRepo.SUMMARY_NAME,
from_analysis=self.SUMMARY_STUDY_NAME)].scans.keys())
self.assertEqual(expected_visit_filesets, visit_fileset_names)
# Check project summary directories were created properly in cache
expected_proj_filesets = ['analysis_sink']
project_dir = self.session_cache(
subject=XnatRepo.SUMMARY_NAME,
visit=XnatRepo.SUMMARY_NAME,
from_analysis=self.SUMMARY_STUDY_NAME)
self.assertEqual(filter_scans(os.listdir(project_dir)),
[(e + '-' + e) for e in expected_proj_filesets])
# and on XNAT
project_fileset_names = filter_scans(
login.projects[self.project].experiments[self.session_label(
subject=XnatRepo.SUMMARY_NAME,
visit=XnatRepo.SUMMARY_NAME,
from_analysis=self.SUMMARY_STUDY_NAME)].scans.keys())
self.assertEqual(expected_proj_filesets, project_fileset_names)
# Reload the data from the summary directories
reloadinputnode = pe.Node(
IdentityInterface(['subject_id', 'visit_id']), 'reload_inputnode')
reloadinputnode.inputs.subject_id = self.SUBJECT
reloadinputnode.inputs.visit_id = self.VISIT
reloadsource_per_subject = pe.Node(RepositorySource(
analysis.bound_spec(f).slice for f in subject_sink_files),
name='reload_source_per_subject')
reloadsource_per_visit = pe.Node(RepositorySource(
analysis.bound_spec(f).slice for f in visit_sink_files),
name='reload_source_per_visit')
reloadsource_per_dataset = pe.Node(RepositorySource(
analysis.bound_spec(f).slice for f in analysis_sink_files),
name='reload_source_per_dataset')
reloadsink = pe.Node(RepositorySink(
(analysis.bound_spec(f).slice
for f in ['resink1', 'resink2', 'resink3']), dummy_pipeline),
name='reload_sink')
reloadsink.inputs.name = 'reload_summary'
reloadsink.inputs.desc = (
"Tests the reloading of subject and project summary filesets")
reloadworkflow = pe.Workflow('reload_summary_unittest',
base_dir=self.work_dir)
for node in (reloadsource_per_subject, reloadsource_per_visit,
reloadsource_per_dataset, reloadsink):
for iterator in ('subject_id', 'visit_id'):
reloadworkflow.connect(reloadinputnode, iterator, node,
iterator)
reloadworkflow.connect(reloadsource_per_subject,
'subject_sink' + PATH_SUFFIX, reloadsink,
'resink1' + PATH_SUFFIX)
reloadworkflow.connect(reloadsource_per_visit,
'visit_sink' + PATH_SUFFIX, reloadsink,
'resink2' + PATH_SUFFIX)
reloadworkflow.connect(reloadsource_per_dataset,
'analysis_sink' + PATH_SUFFIX, reloadsink,
'resink3' + PATH_SUFFIX)
reloadworkflow.run()
# Check that the filesets
self.assertEqual(
filter_scans(
os.listdir(
self.session_cache(
from_analysis=self.SUMMARY_STUDY_NAME))),
['resink1-resink1', 'resink2-resink2', 'resink3-resink3'])
# and on XNAT
with self._connect() as login:
resinked_fileset_names = filter_scans(
login.projects[self.project].experiments[self.session_label(
from_analysis=self.SUMMARY_STUDY_NAME)].scans.keys())
self.assertEqual(sorted(resinked_fileset_names),
['resink1', 'resink2', 'resink3'])
def test_checksums(self):
"""
Tests check of downloaded checksums to see if file needs to be
redownloaded
"""
cache_dir = op.join(self.work_dir, 'cache-checksum-check')
DATASET_NAME = 'source1'
STUDY_NAME = 'checksum_check_analysis'
fileset_fname = DATASET_NAME + text_format.extension
source_target_path = op.join(self.session_cache(cache_dir),
DATASET_NAME + '-' + DATASET_NAME)
md5_path = source_target_path + XnatRepo.MD5_SUFFIX
source_target_fpath = op.join(source_target_path, fileset_fname)
shutil.rmtree(cache_dir, ignore_errors=True)
os.makedirs(cache_dir)
source_repository = XnatRepo(server=SERVER, cache_dir=cache_dir)
source_dataset = source_repository.dataset(self.project)
sink_repository = XnatRepo(server=SERVER, cache_dir=cache_dir)
sink_dataset = sink_repository.dataset(self.checksum_sink_project,
subject_ids=['SUBJECT'],
visit_ids=['VISIT'],
fill_tree=True)
analysis = DummyAnalysis(STUDY_NAME,
dataset=sink_dataset,
processor=SingleProc('ad'),
inputs=[
FilesetFilter(DATASET_NAME,
DATASET_NAME,
text_format,
dataset=source_dataset)
])
source = pe.Node(RepositorySource(
[analysis.bound_spec(DATASET_NAME).slice]),
name='checksum_check_source')
source.inputs.subject_id = self.SUBJECT
source.inputs.visit_id = self.VISIT
source.run()
self.assertTrue(op.exists(md5_path))
self.assertTrue(op.exists(source_target_fpath))
with open(md5_path) as f:
checksums = json.load(f)
# Stash the downloaded file in a new location and create a dummy
# file instead
stash_path = source_target_path + '.stash'
shutil.move(source_target_path, stash_path)
os.mkdir(source_target_path)
with open(source_target_fpath, 'w') as f:
f.write('dummy')
# Run the download, which shouldn't download as the checksums are the
# same
source.run()
with open(source_target_fpath) as f:
d = f.read()
self.assertEqual(d, 'dummy')
# Replace the checksum with a dummy
os.remove(md5_path)
checksums['.'] = 'dummy_checksum'
with open(md5_path, 'w', **JSON_ENCODING) as f:
json.dump(checksums, f, indent=2)
# Retry the download, which should now download since the checksums
# differ
source.run()
with open(source_target_fpath) as f:
d = f.read()
with open(op.join(stash_path, fileset_fname)) as f:
e = f.read()
self.assertEqual(d, e)
# Resink the source file and check that the generated MD5 checksum is
# stored in identical format
DATASET_NAME = 'sink1'
dummy_pipeline = analysis.dummy_pipeline()
dummy_pipeline.cap()
sink = pe.Node(RepositorySink(
[analysis.bound_spec(DATASET_NAME).slice], dummy_pipeline),
name='checksum_check_sink')
sink.inputs.name = 'checksum_check_sink'
sink.inputs.desc = "Tests the generation of MD5 checksums"
sink.inputs.subject_id = self.SUBJECT
sink.inputs.visit_id = self.VISIT
sink.inputs.sink1_path = source_target_fpath
sink_target_path = op.join(
self.session_cache(cache_dir,
project=self.checksum_sink_project,
subject=(self.SUBJECT),
from_analysis=STUDY_NAME),
DATASET_NAME + '-' + DATASET_NAME)
sink_md5_path = sink_target_path + XnatRepo.MD5_SUFFIX
sink.run()
with open(md5_path) as f:
source_checksums = json.load(f)
with open(sink_md5_path) as f:
sink_checksums = json.load(f)
self.assertEqual(
source_checksums, sink_checksums,
("Source checksum ({}) did not equal sink checksum ({})".format(
source_checksums, sink_checksums)))
def test_delayed_download(self):
"""
Tests handling of race conditions where separate processes attempt to
cache the same fileset
"""
cache_dir = op.join(self.work_dir, 'cache-delayed-download')
DATASET_NAME = 'source1'
target_path = op.join(self.session_cache(cache_dir), DATASET_NAME,
DATASET_NAME + text_format.extension)
tmp_dir = target_path + '.download'
shutil.rmtree(cache_dir, ignore_errors=True)
os.makedirs(cache_dir)
repository = XnatRepo(server=SERVER, cache_dir=cache_dir)
dataset = repository.dataset(self.project)
analysis = DummyAnalysis(
self.STUDY_NAME,
dataset,
SingleProc('ad'),
inputs=[FilesetFilter(DATASET_NAME, DATASET_NAME, text_format)])
source = pe.Node(RepositorySource(
[analysis.bound_spec(DATASET_NAME).slice]),
name='delayed_source')
source.inputs.subject_id = self.SUBJECT
source.inputs.visit_id = self.VISIT
result1 = source.run()
source1_path = result1.outputs.source1_path
self.assertTrue(op.exists(source1_path))
self.assertEqual(
source1_path, target_path,
"Output file path '{}' not equal to target path '{}'".format(
source1_path, target_path))
# Clear cache to start again
shutil.rmtree(cache_dir, ignore_errors=True)
# Create tmp_dir before running interface, this time should wait for 1
# second, check to see that the session hasn't been created and then
# clear it and redownload the fileset.
os.makedirs(tmp_dir)
source.inputs.race_cond_delay = 1
result2 = source.run()
source1_path = result2.outputs.source1_path
# Clear cache to start again
shutil.rmtree(cache_dir, ignore_errors=True)
# Create tmp_dir before running interface, this time should wait for 1
# second, check to see that the session hasn't been created and then
# clear it and redownload the fileset.
internal_dir = op.join(tmp_dir, 'internal')
deleted_tmp_dir = tmp_dir + '.deleted'
def simulate_download():
"Simulates a download in a separate process"
os.makedirs(internal_dir)
time.sleep(5)
# Modify a file in the temp dir to make the source download keep
# waiting
logger.info('Updating simulated download directory')
with open(op.join(internal_dir, 'download'), 'a') as f:
f.write('downloading')
time.sleep(10)
# Simulate the finalising of the download by copying the previously
# downloaded file into place and deleting the temp dir.
logger.info('Finalising simulated download')
with open(target_path, 'a') as f:
f.write('simulated')
shutil.move(tmp_dir, deleted_tmp_dir)
source.inputs.race_cond_delay = 10
p = Process(target=simulate_download)
p.start() # Start the simulated download in separate process
time.sleep(1)
source.run() # Run the local download
p.join()
with open(op.join(deleted_tmp_dir, 'internal', 'download')) as f:
d = f.read()
self.assertEqual(d, 'downloading')
with open(target_path) as f:
d = f.read()
self.assertEqual(d, 'simulated')
WORK_PATH = os.path.join('/scratch', 'dq13', 'aspree', 'qsm')
CACHE_PROJECT_PATH = os.path.join(WORK_PATH, 'project.pkl')
try:
os.makedirs(WORK_PATH)
except OSError as e:
if e.errno != errno.EEXIST:
raise
session_ids_path = os.path.join(
os.path.dirname(os.path.realpath(__file__)), '..', 'resources',
'old_swi_coils_remaining.txt')
print(session_ids_path)
with open(session_ids_path) as f:
ids = f.read().split()
PROJECT_ID = 'MRH017'
filesets = {FilesetFilter('coils', 'swi_coils', zip_format)}
visit_ids = visit_ids['MR01']
repository = XnatRepo(cache_dir='/scratch/dq13/xnat_cache3')
if args.cache_project:
project = repository.project(PROJECT_ID, subject_ids=ids,
visit_ids=visit_ids)
with open(CACHE_PROJECT_PATH, 'w') as f:
pkl.dump(project, f)
else:
with open(CACHE_PROJECT_PATH) as f:
project = pkl.load(f)
repository.cache(PROJECT_ID, filesets.values(), subject_ids=ids,
