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from mock import Mock, patch |
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from datetime import datetime as dt |
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from tests.ditest import DependencyInjectionTestBase |
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class LoggingTests(DependencyInjectionTestBase): |
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def setUp(self): |
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super(LoggingTests, self).setUp() |
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self.repo.knowsByLocation.return_value = True |
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self.opts = Mock() |
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self.opts.dryrun = False |
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img = Mock() |
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img.provenance = {'acquired':dt.now(), |
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'subject':'JD', |
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'protocol':'X', |
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'technique':'abc', |
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'repetition-time':1.0, |
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'epi-factor':1.0, |
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'magnetization-transfer-contrast':True, |
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'diffusion':True, |
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'echo-time':123, |
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'flip-angle':892, |
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'inversion-time':123} |
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self.locationFactory.completeString.side_effect = lambda p: p |
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self.repo.byLocation.return_value = img |
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self.provenancesAdded = [] |
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def wrapProv(location, transient=False, provenance=False, dependencies=None): |
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self.provenancesAdded.append(provenance) |
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self.newimg = Mock() |
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self.newimg.provenance = {'acquired':location} |
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return (self.newimg, 'test') |
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self.dependencies.reconfigureOrGetConfiguration.return_value = self.opts |
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patcher = patch('niprov.logging.add') |
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self.add = patcher.start() |
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self.add.side_effect = wrapProv |
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self.addCleanup(patcher.stop) |
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def log(self, *args, **kwargs): |
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from niprov.logging import log |
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return log(*args, dependencies=self.dependencies, opts=self.opts, |
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**kwargs) |
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def test_Returns_img(self): |
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parents = ['/p/f1'] |
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new = '/p/f2' |
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trans = 'Something cool' |
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out = self.log(new, trans, parents) |
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self.assertEqual(out, self.newimg) |
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def test_Copies_fields_from_known_parent(self): |
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self.locationFactory.completeString.side_effect = lambda p: p |
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parent = '/p/f1' |
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parents = [parent] |
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parentProv = {'acquired':dt.now(), |
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'subject':'JD', |
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'protocol':'X', |
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'technique':'abc', |
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'repetition-time':1.0, |
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'epi-factor':1.0, |
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'magnetization-transfer-contrast':True, |
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'diffusion':True, |
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'echo-time':123, |
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'flip-angle':892, |
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'inversion-time':123} |
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parentImg = Mock() |
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parentImg.provenance = parentProv |
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self.repo.byLocation.side_effect = lambda x: {parent:parentImg}[x] |
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self.log('new', 'trans', parents) |
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self.assertEqual(self.provenancesAdded[0]['acquired'], parentProv['acquired']) |
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self.assertEqual(self.provenancesAdded[0]['subject'], parentProv['subject']) |
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self.assertEqual(self.provenancesAdded[0]['protocol'], parentProv['protocol']) |
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self.assertEqual(self.provenancesAdded[0]['technique'], parentProv['technique']) |
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self.assertEqual(self.provenancesAdded[0]['repetition-time'], parentProv['repetition-time']) |
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self.assertEqual(self.provenancesAdded[0]['epi-factor'], parentProv['epi-factor']) |
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self.assertEqual(self.provenancesAdded[0]['magnetization-transfer-contrast'], |
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parentProv['magnetization-transfer-contrast']) |
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self.assertEqual(self.provenancesAdded[0]['diffusion'], parentProv['diffusion']) |
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self.assertEqual(self.provenancesAdded[0]['echo-time'], parentProv['echo-time']) |
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self.assertEqual(self.provenancesAdded[0]['flip-angle'], parentProv['flip-angle']) |
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self.assertEqual(self.provenancesAdded[0]['inversion-time'], parentProv['inversion-time']) |
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def test_Adds_code_or_logtext(self): |
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self.log('new', 'trans', 'old', code='abc', logtext='def') |
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self.assertEqual(self.provenancesAdded[0]['code'],'abc') |
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self.assertEqual(self.provenancesAdded[0]['logtext'],'def') |
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def test_Determines_user_and_logs_them(self): |
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self.users.determineUser.return_value = 'paprika' |
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self.log('new', 'trans', 'old', user='mononoko') |
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self.users.determineUser.assert_called_with('mononoko') |
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self.assertEqual(self.provenancesAdded[0]['user'],'paprika') |
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def test_Script_added_to_provenance(self): |
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parents = ['/p/f1'] |
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new = '/p/f2' |
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trans = 'Something cool' |
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script = '/p/test.py' |
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self.log(new, trans, parents, script=script) |
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self.assertEqual(self.provenancesAdded[0]['script'], script) |
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def test_Accepts_and_processes_custom_provenance(self): |
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parents = ['/p/f1'] |
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new = '/p/f2' |
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trans = 'Something cool' |
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p = {'akey':'avalue'} |
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self.log(new, trans, parents, provenance=p) |
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self.assertEqual(self.provenancesAdded[0]['akey'], 'avalue') |
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def test_Doesnt_complain_if_parent_is_missing_basic_fields(self): |
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img = Mock() |
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img.provenance = {'acquired':dt.now()} #missing subject |
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self.repo.byLocation.return_value = img |
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provenance = self.log('new', 'trans', ['/p/f1parent']) |
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self.assertNotIn('subject', self.provenancesAdded[0]) |
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def test_Calls_reconfigureOrGetConfiguration_on_dependencies(self): |
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outOpts = Mock() |
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outOpts.dryrun = True |
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self.dependencies.reconfigureOrGetConfiguration.return_value = outOpts |
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provenance = self.log(['/p/f1'], 'bla', ['/p/f2'], transient=True) |
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self.dependencies.reconfigureOrGetConfiguration.assert_called_with( |
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self.opts) |
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def test_Can_pass_multiple_new_files(self): |
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parents = ['p1','p2'] |
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new = ['/p/f2','/p/f3'] |
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trans = 'Something cool' |
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self.locationFactory.completeString.side_effect = lambda p: 'l:'+p |
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self.log(new, trans, parents) |
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self.assertEqual(self.provenancesAdded[0]['parents'], ['l:p1','l:p2']) |
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self.assertEqual(self.provenancesAdded[1]['parents'], ['l:p1','l:p2']) |
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def test_Add_parent_if_parent_unknown(self): |
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self.repo.knowsByLocation.return_value = False |
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self.locationFactory.completeString.side_effect = lambda p: 'l:'+p |
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provenance = self.log('new', 'trans', 'parentpath') |
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self.add.assert_any_call('l:parentpath') |
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self.listener.addUnknownParent.assert_called_with('l:parentpath') |
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def test_Uses_validated_location_for_parent_lookup(self): |
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self.locationFactory.completeString.side_effect = lambda p: 'l:'+p |
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provenance = self.log('new', 'trans', 'parentpath') |
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self.repo.knowsByLocation.assert_called_with('l:parentpath') |
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self.repo.byLocation.assert_called_with('l:parentpath') |
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def test_If_parent_unknown_uses_add_return_value(self): |
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"""In this case the parent provenance should be obtained from |
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what add() returns. |
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""" |
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self.repo.knowsByLocation.return_value = False |
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parent = 'unknown/parent/path.f' |
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provenance = self.log('new', 'trans', [parent]) |
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assert not self.repo.byLocation.called |
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loggedFileProv = self.provenancesAdded[1] # [0]: parent [1]: newly logged |
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## add function is mocked to set 'acquired' field to location passed |
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## since acquired is an inheritable field, it should show up in kid: |
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self.assertEqual(loggedFileProv['acquired'], 'unknown/parent/path.f') |
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ilogue /
niprov
