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import unittest |
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import os, shutil |
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from os.path import abspath |
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class ContextApiTests(unittest.TestCase): |
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def setUp(self): |
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self.dbpath = os.path.expanduser(os.path.join('~','provenance_test.json')) |
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if os.path.exists(self.dbpath): |
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os.remove(self.dbpath) |
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os.mkdir('temp') |
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from niprov import Context |
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self.provenance = Context() |
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self.provenance.config.database_type = 'file' |
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self.provenance.config.database_url = self.dbpath |
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def tearDown(self): |
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shutil.rmtree('temp') |
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def touch(self, path): |
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with open(path,'w') as tempfile: |
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tempfile.write('0') |
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def test_Relative_paths(self): |
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self.provenance.discover('testdata') |
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newfile = 'temp/smoothed.test' |
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self.touch(newfile) |
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self.provenance.log(newfile, 'test', 'testdata/eeg/stub.cnt') |
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img = self.provenance.get().byLocation(newfile) |
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View Code Duplication |
def test_Log(self): |
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self.provenance.discover('testdata') |
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newfile = 'temp/smoothed.test' |
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self.touch(newfile) |
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parent = os.path.abspath('testdata/eeg/stub.cnt') |
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self.provenance.log(newfile, 'test', parent) |
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testfpath = os.path.abspath(newfile) |
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img = self.provenance.get().byLocation(testfpath) |
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self.assertEqual(img.provenance['subject'], 'Jane Doe') |
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self.assertEqual(img.provenance['size'], os.path.getsize(newfile)) |
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View Code Duplication |
def test_Record_with_user(self): |
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self.provenance.discover('testdata') |
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newfile = 'temp/recorded.test' |
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self.touch(newfile) |
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parent = os.path.abspath('testdata/eeg/stub.cnt') |
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self.provenance.record('echo hallo', newfile, parent, user='007') |
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testfpath = os.path.abspath(newfile) |
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img = self.provenance.get().byLocation(testfpath) |
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self.assertEqual(img.provenance['user'], '007') |
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def test_Export_Import(self): |
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from niprov.exceptions import UnknownFileError |
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self.provenance.discover('testdata') |
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discoveredFile = os.path.abspath('testdata/eeg/stub.cnt') |
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self.assertIsNotNone(self.provenance.get().byLocation(discoveredFile)) |
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backupFilepath = self.provenance.backup() |
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os.remove(self.dbpath) # get rid of existing data. |
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with self.assertRaises(IndexError): |
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self.provenance.get().byLocation(discoveredFile) |
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self.provenance.importp(backupFilepath) |
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self.assertIsNotNone(self.provenance.get().byLocation(discoveredFile)) |
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@unittest.skip("Doesn't work on Travis right now.") |
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def test_Attach_provenance_string_in_file_based_on_config(self): |
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import nibabel |
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self.provenance.config.attach = True |
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newfile = os.path.abspath('temp/fileX.nii.gz') |
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shutil.copy('testdata/nifti/fieldmap.nii.gz', newfile) |
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self.provenance.add(newfile) |
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img = nibabel.load(newfile) |
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self.assertEqual(img.get_header().extensions.count('comment'), 1) |
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self.assertEqual(img.get_header().extensions[0].get_code(), 6) |
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content = img.get_header().extensions[0].get_content() |
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self.assertIn('"path": "{0}"'.format(newfile), content) |
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def test_Approval(self): |
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self.provenance.discover('testdata') |
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self.provenance.markForApproval([os.path.abspath('testdata/dicom/T1.dcm'), |
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os.path.abspath('testdata/dicom/T2.dcm')]) |
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imgs = self.provenance.markedForApproval() |
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self.provenance.approve(os.path.abspath('testdata/dicom/T1.dcm')) |
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imgs = self.provenance.markedForApproval() |
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def test_Comparison(self): |
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# Given two PARREC images' provenance records |
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par1 = self.provenance.add(abspath('testdata/parrec/T1.PAR'))[0] |
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par2 = self.provenance.add(abspath('testdata/parrec/T2.PAR'))[0] |
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# Comparing them returns a Diff object with methods testing equality |
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self.assertFalse(self.provenance.compare(par1, par2).areEqual()) |
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# Compare() can also be called as a method on the objects themselves, |
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# and the Diff object has assert..() methods that raise AssertionErrors |
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msgRegExp = ".*echo-time.*2\.08.*80\.0.*" |
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with self.assertRaisesRegexp(AssertionError, msgRegExp): |
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par1.compare(par2).assertEqualProtocol() |
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def test_Search(self): |
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x1, s = self.provenance.add('x1', transient=True, |
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provenance={'transformation':'needle and thread'}) |
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x2, s = self.provenance.add('x2/needle.y', transient=True, |
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provenance={'transformation':'needle and thread'}) |
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x3, s = self.provenance.add('x3', transient=True, |
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provenance={'transformation':'hammer and tongs'}) |
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results = self.provenance.search('needle') |
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self.assertEqual(len(results), 2) |
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self.assertEqual(x2.provenance['id'], results[0].provenance['id']) |
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self.assertEqual(x1.provenance['id'], results[1].provenance['id']) |
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def test_GetModalities(self): |
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self.provenance.discover('testdata') |
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modalities = self.provenance.get().allModalities() |
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self.assertIn('MRI', modalities) |
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self.assertIn('DWI', modalities) |
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self.assertIn('EEG', modalities) |
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if __name__ == '__main__': |
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unittest.main() |
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ilogue /
niprov
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