class MongoTests(unittest.TestCase):
def setUp(self):
from niprov import ProvenanceContext
self.provenance = ProvenanceContext()
self.fullURL = URL.format(PASSWORD)
self.provenance.config.database_type = 'MongoDB'
self.provenance.config.database_url = self.fullURL
def tearDown(self):
client = MongoClient(self.fullURL)
client.get_default_database().provenance.drop()
@unittest.skipIf("TRAVIS" in os.environ, "Skipping this test on Travis CI.")
def test_Something(self):
self.provenance.discover('testdata')
testfpath = os.path.abspath('testdata/parrec/T1.PAR')
img = self.provenance.get().byLocation(testfpath)
self.assertEqual(img.provenance['subject'], '05aug14test')
@unittest.skipIf("TRAVIS" in os.environ, "Skipping this test on Travis CI.")
def test_Stats(self):
self.provenance.discover('testdata')
repository = self.provenance.deps.getRepository()
print(repository.statistics())
class MongoTests(unittest.TestCase):
def setUp(self):
from niprov import ProvenanceContext
self.provenance = ProvenanceContext()
self.fullURL = URL.format(PASSWORD)
self.provenance.config.database_type = 'MongoDB'
self.provenance.config.database_url = self.fullURL
def tearDown(self):
client = MongoClient(self.fullURL)
client.get_default_database().provenance.drop()
@unittest.skipIf("TRAVIS" in os.environ,
"Skipping this test on Travis CI.")
def test_Something(self):
self.provenance.discover('testdata')
testfpath = os.path.abspath('testdata/parrec/T1.PAR')
img = self.provenance.get().byLocation(testfpath)
self.assertEqual(img.provenance['subject'], '05aug14test')
@unittest.skipIf("TRAVIS" in os.environ,
"Skipping this test on Travis CI.")
def test_Stats(self):
self.provenance.discover('testdata')
repository = self.provenance.deps.getRepository()
print(repository.statistics())
class TerminalApiTests(unittest.TestCase):
def setUp(self):
self.dbpath = os.path.expanduser(
os.path.join('~', 'provenance_test.json'))
if os.path.exists(self.dbpath):
os.remove(self.dbpath)
os.mkdir('temp')
from niprov import ProvenanceContext
self.provenance = ProvenanceContext()
self.provenance.config.database_type = 'file'
self.provenance.config.database_url = self.dbpath
self.provenance.config.verbose = False
self.oldstdout = sys.stdout
sys.stdout = self.stdout = StringIO()
def tearDown(self):
sys.stdout = self.oldstdout
self.stdout.close()
shutil.rmtree('temp')
@unittest.skip("Doesn't work on travis")
def test_Report_pipeline(self):
self.provenance.discover('testdata')
raw = os.path.abspath('testdata/eeg/stub.cnt')
self.provenance.log(absp('p1a.f'), 'test', raw, transient=True)
self.provenance.log(absp('p1b.f'), 'test', raw, transient=True)
self.provenance.log(absp('p2.f'),
'test',
absp('p1a.f'),
transient=True)
self.provenance.export(None, 'stdout', 'simple', pipeline=True)
exp = ''
exp += '+---stub.cnt\n'
exp += '| +---p1a.f\n'
exp += '| | +---p2.f\n'
#exp += '| +---p1b.f\n' # p1b is not related to p2f
import time
time.sleep(0.3)
self.assertIn(exp, self.stdout.getvalue())
class TerminalApiTests(unittest.TestCase):
def setUp(self):
self.dbpath = os.path.expanduser(os.path.join('~','provenance_test.json'))
if os.path.exists(self.dbpath):
os.remove(self.dbpath)
os.mkdir('temp')
from niprov import ProvenanceContext
self.provenance = ProvenanceContext()
self.provenance.config.database_type = 'file'
self.provenance.config.database_url = self.dbpath
self.provenance.config.verbose = False
self.oldstdout = sys.stdout
sys.stdout = self.stdout = StringIO()
def tearDown(self):
sys.stdout = self.oldstdout
self.stdout.close()
shutil.rmtree('temp')
@unittest.skip("Doesn't work on travis")
def test_Report_pipeline(self):
self.provenance.discover('testdata')
raw = os.path.abspath('testdata/eeg/stub.cnt')
self.provenance.log(absp('p1a.f'), 'test', raw, transient=True)
self.provenance.log(absp('p1b.f'), 'test', raw, transient=True)
self.provenance.log(absp('p2.f'), 'test', absp('p1a.f'), transient=True)
self.provenance.export(None, 'stdout', 'simple', pipeline=True)
exp = ''
exp += '+---stub.cnt\n'
exp += '| +---p1a.f\n'
exp += '| | +---p2.f\n'
#exp += '| +---p1b.f\n' # p1b is not related to p2f
import time
time.sleep(0.3)
self.assertIn(exp, self.stdout.getvalue())
class ProvenanceContextApiTests(unittest.TestCase):
def setUp(self):
self.dbpath = os.path.expanduser(os.path.join('~','provenance_test.json'))
if os.path.exists(self.dbpath):
os.remove(self.dbpath)
os.mkdir('temp')
from niprov import ProvenanceContext
self.provenance = ProvenanceContext()
self.provenance.config.database_type = 'file'
self.provenance.config.database_url = self.dbpath
def tearDown(self):
shutil.rmtree('temp')
def touch(self, path):
with open(path,'w') as tempfile:
tempfile.write('0')
def test_Relative_paths(self):
self.provenance.discover('testdata')
newfile = 'temp/smoothed.test'
self.touch(newfile)
self.provenance.log(newfile, 'test', 'testdata/eeg/stub.cnt')
img = self.provenance.get().byLocation(newfile)
def test_Log(self):
self.provenance.discover('testdata')
newfile = 'temp/smoothed.test'
self.touch(newfile)
parent = os.path.abspath('testdata/eeg/stub.cnt')
self.provenance.log(newfile, 'test', parent)
testfpath = os.path.abspath(newfile)
img = self.provenance.get().byLocation(testfpath)
self.assertEqual(img.provenance['subject'], 'Jane Doe')
self.assertEqual(img.provenance['size'], os.path.getsize(newfile))
def test_Record_with_user(self):
self.provenance.discover('testdata')
newfile = 'temp/recorded.test'
self.touch(newfile)
parent = os.path.abspath('testdata/eeg/stub.cnt')
self.provenance.record('echo hallo', newfile, parent, user='******')
testfpath = os.path.abspath(newfile)
img = self.provenance.get().byLocation(testfpath)
self.assertEqual(img.provenance['user'], '007')
def test_Export_Import(self):
from niprov.exceptions import UnknownFileError
self.provenance.discover('testdata')
discoveredFile = os.path.abspath('testdata/eeg/stub.cnt')
self.assertIsNotNone(self.provenance.get().byLocation(discoveredFile))
backupFilepath = self.provenance.backup()
os.remove(self.dbpath) # get rid of existing data.
self.assertIsNone(self.provenance.get().byLocation(discoveredFile))
self.provenance.importp(backupFilepath)
self.assertIsNotNone(self.provenance.get().byLocation(discoveredFile))
@unittest.skip("Doesn't work on Travis right now.")
def test_Attach_provenance_string_in_file_based_on_config(self):
import nibabel
self.provenance.config.attach = True
newfile = os.path.abspath('temp/fileX.nii.gz')
shutil.copy('testdata/nifti/fieldmap.nii.gz', newfile)
self.provenance.add(newfile)
img = nibabel.load(newfile)
self.assertEqual(img.get_header().extensions.count('comment'), 1)
self.assertEqual(img.get_header().extensions[0].get_code(), 6)
content = img.get_header().extensions[0].get_content()
self.assertIn('"path": "{0}"'.format(newfile), content)
def test_Approval(self):
self.provenance.discover('testdata')
self.provenance.markForApproval(['testdata/parrec/T1.PAR',
'testdata/parrec/T2.PAR'])
imgs = self.provenance.markedForApproval()
self.provenance.approve('testdata/parrec/T1.PAR')
imgs = self.provenance.markedForApproval()
def test_Comparison(self):
# Given two PARREC images' provenance records
par1 = self.provenance.add(abspath('testdata/parrec/T1.PAR'))
par2 = self.provenance.add(abspath('testdata/parrec/T2.PAR'))
# Comparing them returns a Diff object with methods testing equality
self.assertFalse(self.provenance.compare(par1, par2).areEqual())
# Compare() can also be called as a method on the objects themselves,
# and the Diff object has assert..() methods that raise AssertionErrors
msgRegExp = ".*echo-time.*2\.08.*80\.0.*"
with self.assertRaisesRegexp(AssertionError, msgRegExp):
par1.compare(par2).assertEqualProtocol()
def test_Search(self):
x1 = self.provenance.add('x1', transient=True,
provenance={'transformation':'needle and thread'})
x2 = self.provenance.add('x2/needle.y', transient=True,
provenance={'transformation':'needle and thread'})
x3 = self.provenance.add('x3', transient=True,
provenance={'transformation':'hammer and tongs'})
results = self.provenance.search('needle')
self.assertEqual(len(results), 2)
self.assertEqual(x2.provenance['id'], results[0].provenance['id'])
self.assertEqual(x1.provenance['id'], results[1].provenance['id'])
def test_GetModalities(self):
self.provenance.discover('testdata')
modalities = self.provenance.get().allModalities()
self.assertIn('MRI', modalities)
self.assertIn('DWI', modalities)
self.assertIn('EEG', modalities)
def test_Version_history(self):
self.provenance.add('f', transient=True, provenance={'a':1})
img = self.provenance.get().byLocation('f')
self.assertEqual(1, img.provenance['a'])
self.provenance.add('f', transient=True, provenance={'a':2})
img = self.provenance.get().byLocation('f')
self.assertEqual(2, img.provenance['a'])
self.assertEqual(1, img.versions[-1]['a'])
self.provenance.add('f', transient=True, provenance={'a':3})
img = self.provenance.get().byLocation('f')
self.assertEqual(3, img.provenance['a'])
self.assertEqual(2, img.versions[-1]['a'])
self.assertEqual(1, img.versions[-2]['a'])
def test_If_no_parent_provided_found_copy_considered_parent(self):
self.provenance.add('testdata/eeg/stub.cnt')
self.touch('temp/orig.f')
self.provenance.log('temp/orig.f', 'op1', 'testdata/eeg/stub.cnt')
shutil.copy('temp/orig.f', 'temp/copy.f')
self.touch('temp/child.f')
child = self.provenance.log('temp/child.f', 'op2', 'temp/copy.f')
self.assertEqual(child.provenance['subject'], 'Jane Doe')
copy = self.provenance.get().byLocation('temp/copy.f')
self.assertIn('temp/orig.f', copy.provenance['parents'][0])
def test_Differentiates_Fifs(self):
"""
The fields tested here are just a subset.
"""
PROJDESC = 'ECG-planar-999--0.080-0.080-PCA-01'
fiftypes = {'ave': {'fif-type':'ave', 'dimensions':[2,401,701]},
'cov': {'fif-type':'cov', 'dimensions':[366, 366]},
'epo': {'fif-type':'epo', 'highpass':0.10000000149011612},
'fwd': {'fif-type':'fwd'},
'trans': {'fif-type':'trans'},
'proj' : {'fif-type':'proj',
'projection-description':PROJDESC}}
for ftype, fields in fiftypes.items():
pth = os.path.abspath('testdata/fif/test-{}.fif'.format(ftype))
img = self.provenance.add(pth)
for field, expectedValue in fields.items():
self.assertIn(field, img.provenance)
self.assertEqual(img.provenance[field], expectedValue)