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)