ContextApiTests

Complexity

Total Complexity

13

Size/Duplication

Total Lines	84
Duplicated Lines	22.62 %

9 Methods

Rating	Name	Duplication	Size	Complexity
A	setUp()	0	9	2
A	touch()	0	3	2
A	tearDown()	0	2	1
A	test_Approval()	0	7	1
A	test_Export_Import()	0	11	2
A	test_Comparison()	0	11	2
A	test_Log()	10	10	1
A	test_Record_with_user()	9	9	1
A	test_Attach_provenance_string_in_file_based_on_config()	0	12	1

import unittest
import os, shutil
from os.path import abspath


class ContextApiTests(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 Context
        self.provenance = Context()
        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_Log(self):

This code seems to be duplicated in your project.

        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(forFile=testfpath)
        self.assertEqual(img.provenance['subject'], 'Jane Doe')
        self.assertEqual(img.provenance['size'], os.path.getsize(newfile))

    def test_Record_with_user(self):

This code seems to be duplicated in your project.

        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='007')
        testfpath = os.path.abspath(newfile)
        img = self.provenance.get(forFile=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(forFile=discoveredFile))
        backupFilepath = self.provenance.backup()
        os.remove(self.dbpath) # get rid of existing data.
        with self.assertRaises(UnknownFileError):
            self.provenance.get(forFile=discoveredFile)
        self.provenance.importp(backupFilepath)
        self.assertIsNotNone(self.provenance.get(forFile=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([os.path.abspath('testdata/dicom/T1.dcm'),
                                os.path.abspath('testdata/dicom/T2.dcm')])
        imgs = self.provenance.markedForApproval()
        self.provenance.approve(os.path.abspath('testdata/dicom/T1.dcm'))
        imgs = self.provenance.markedForApproval()

    def test_Comparison(self):
        # Given two PARREC images' provenance records
        par1 = self.provenance.add(abspath('testdata/parrec/T1.PAR'))[0]
        par2 = self.provenance.add(abspath('testdata/parrec/T2.PAR'))[0]
        # 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()


if __name__ == '__main__':
    unittest.main()