Beispiel #1
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 def test_byLocation(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'location':'1','path':'a'})
     img2 = self.imageWithProvenance({'location':'2','path':'b'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2]
     out = repo.byLocation('2')
     self.assertEqual(img2, out)
Beispiel #2
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 def test_getSeries_returns_None_right_away_if_no_series_id(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img = Mock()
     img.getSeriesId.return_value = None
     repo.all = Mock()
     out = repo.getSeries(img)
     assert not repo.all.called, "Should not be called if no series id"
     self.assertEqual(None, out)
Beispiel #3
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 def test_byLocation(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'location': '1', 'path': 'a'})
     img2 = self.imageWithProvenance({'location': '2', 'path': 'b'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2]
     out = repo.byLocation('2')
     self.assertEqual(img2, out)
Beispiel #4
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 def test_getSeries_returns_None_right_away_if_no_series_id(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img = Mock()
     img.getSeriesId.return_value = None
     repo.all = Mock()
     out = repo.getSeries(img)
     assert not repo.all.called, "Should not be called if no series id"
     self.assertEqual(None, out)
Beispiel #5
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 def test_Search_only_returns_objects_which_have_needle(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'transformation':'green blue'})
     img2 = self.imageWithProvenance({'transformation':'yellow red'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2]
     out = repo.search('red')
     self.assertEqual([img2], out)
Beispiel #6
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 def test_byId(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'id': '1'})
     img2 = self.imageWithProvenance({'id': '2'})
     img3 = self.imageWithProvenance({'id': '3'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3]
     out = repo.byId('2')
     self.assertEqual(img2, out)
Beispiel #7
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 def test_byId(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'id':'1'})
     img2 = self.imageWithProvenance({'id':'2'})
     img3 = self.imageWithProvenance({'id':'3'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3]
     out = repo.byId('2')
     self.assertEqual(img2, out)
Beispiel #8
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 def test_Search_only_returns_objects_which_have_needle(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'transformation': 'green blue'})
     img2 = self.imageWithProvenance({'transformation': 'yellow red'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2]
     out = repo.search('red')
     self.assertEqual([img2], out)
Beispiel #9
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 def test_Add(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'location': '1', 'foo': 'baz'})
     repo.all = Mock()
     repo.all.return_value = [img1]
     image = self.imageWithProvenance({'location': '2', 'foo': 'bar'})
     repo.add(image)
     self.serializer.serializeList.assert_called_with([img1, image])
     self.filesys.write.assert_called_with(repo.datafile,
                                           self.serializer.serializeList())
Beispiel #10
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 def test_getSeries(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img = Mock()
     img.getSeriesId.return_value = '2'
     img1 = self.imageWithProvenance({'seriesuid':'1','path':'a'})
     img2 = self.imageWithProvenance({'seriesuid':'2','path':'b'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2]
     out = repo.getSeries(img)
     self.assertEqual(img2, out)
Beispiel #11
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 def test_Search_returns_max_20_results(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     recs = []
     for i in range(35):
         recs.append(self.imageWithProvenance({'transformation':'red'}))
     repo.all = Mock()
     repo.all.return_value = recs
     out = repo.search('red')
     self.assertEqual(20, len(out))
Beispiel #12
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 def test_Search_distinguishes_words_as_OR_search(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     i1 = self.imageWithProvenance({'transformation':'blue red red'})       #2
     i2 = self.imageWithProvenance({'transformation':'red blue green red'}) #3
     i3 = self.imageWithProvenance({'transformation':'green blue'})         #1
     repo.all = Mock()
     repo.all.return_value = [i1,i2,i3]
     out = repo.search('red green')
     self.assertEqual([i2, i1, i3], out)
Beispiel #13
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 def test_getSeries(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img = Mock()
     img.getSeriesId.return_value = '2'
     img1 = self.imageWithProvenance({'seriesuid': '1', 'path': 'a'})
     img2 = self.imageWithProvenance({'seriesuid': '2', 'path': 'b'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2]
     out = repo.getSeries(img)
     self.assertEqual(img2, out)
Beispiel #14
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 def test_Search_returns_max_20_results(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     recs = []
     for i in range(35):
         recs.append(self.imageWithProvenance({'transformation': 'red'}))
     repo.all = Mock()
     repo.all.return_value = recs
     out = repo.search('red')
     self.assertEqual(20, len(out))
Beispiel #15
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 def test_Search_distinguishes_words_as_OR_search(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     i1 = self.imageWithProvenance({'transformation': 'blue red red'})  #2
     i2 = self.imageWithProvenance({'transformation':
                                    'red blue green red'})  #3
     i3 = self.imageWithProvenance({'transformation': 'green blue'})  #1
     repo.all = Mock()
     repo.all.return_value = [i1, i2, i3]
     out = repo.search('red green')
     self.assertEqual([i2, i1, i3], out)
Beispiel #16
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 def test_latest(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'added':datetime.datetime(1982, 1, 5)})
     img2 = self.imageWithProvenance({'added':datetime.datetime(1982, 2, 5)})
     img3 = self.imageWithProvenance({'added':datetime.datetime(1982, 3, 5)})
     img4 = self.imageWithProvenance({'added':datetime.datetime(1982, 4, 5)})
     img5 = self.imageWithProvenance({'added':datetime.datetime(1982, 5, 5)})
     repo.all = Mock()
     repo.all.return_value = [img1,img2,img3,img4,img5]
     out = repo.latest(3)
     self.assertEqual([img5, img4, img3], out)
Beispiel #17
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 def test_updateApproval(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img = Mock()
     img.provenance = {'fiz':'baf','approval':'notsure'}
     def assertion(img):
         self.assertEqual({'fiz':'baf','approval':'excellent!'}, img.provenance)
     repo.byLocation = Mock()
     repo.byLocation.return_value = img
     repo.update = Mock()
     repo.update.side_effect = assertion
     repo.updateApproval('/p/f1','excellent!')
Beispiel #18
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 def test_Add(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'location':'1','foo':'baz'})
     repo.all = Mock()
     repo.all.return_value = [img1]
     image = self.imageWithProvenance({'location': '2','foo':'bar'})
     repo.add(image)
     self.serializer.serializeList.assert_called_with(
         [img1, image])
     self.filesys.write.assert_called_with(repo.datafile, 
         self.serializer.serializeList())
Beispiel #19
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 def test_Search_sorts_results_by_number_of_matches(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'transformation':'red bluered'})
     img2 = self.imageWithProvenance({'transformation':'red and green'})
     img3 = self.imageWithProvenance({'transformation':'red pruple red red'})
     img4 = self.imageWithProvenance({'transformation':'nuthin'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3, img4]
     out = repo.search('red')
     self.assertEqual([img3, img1, img2], out)
Beispiel #20
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 def test_Search_sorts_results_by_number_of_matches(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'transformation': 'red bluered'})
     img2 = self.imageWithProvenance({'transformation': 'red and green'})
     img3 = self.imageWithProvenance(
         {'transformation': 'red pruple red red'})
     img4 = self.imageWithProvenance({'transformation': 'nuthin'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3, img4]
     out = repo.search('red')
     self.assertEqual([img3, img1, img2], out)
Beispiel #21
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 def test_stats(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     repo.all = Mock()
     records = [{},{},{},{},{},{},{},{},{},{},{}]
     totalsize = 0
     for r in records:
         r['size'] = random.randint(1,1000)
         totalsize += r['size']
     repo.all.return_value = [self.imageWithProvenance(r) for r in records]
     out = repo.statistics()
     self.assertEqual(11, out['count'])
     self.assertEqual(totalsize, out['totalsize'])
Beispiel #22
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 def test_stats(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     repo.all = Mock()
     records = [{}, {}, {}, {}, {}, {}, {}, {}, {}, {}, {}]
     totalsize = 0
     for r in records:
         r['size'] = random.randint(1, 1000)
         totalsize += r['size']
     repo.all.return_value = [self.imageWithProvenance(r) for r in records]
     out = repo.statistics()
     self.assertEqual(11, out['count'])
     self.assertEqual(totalsize, out['totalsize'])
Beispiel #23
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 def test_byLocations(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p['a']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'location':'i'})
     img2 = self.imageWithProvenance({'location':'j'})
     img3 = self.imageWithProvenance({'location':'m'})
     img4 = self.imageWithProvenance({'location':'f'})
     img5 = self.imageWithProvenance({'location':'x'})
     repo.all = Mock()
     repo.all.return_value = [img1,img2,img3,img4,img5]
     out = repo.byLocations(['j','f','k'])
     self.assertEqual([img2, img4], out)
Beispiel #24
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 def test_byLocations(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p['a']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'location': 'i'})
     img2 = self.imageWithProvenance({'location': 'j'})
     img3 = self.imageWithProvenance({'location': 'm'})
     img4 = self.imageWithProvenance({'location': 'f'})
     img5 = self.imageWithProvenance({'location': 'x'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3, img4, img5]
     out = repo.byLocations(['j', 'f', 'k'])
     self.assertEqual([img2, img4], out)
Beispiel #25
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 def test_byParents(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'parents':[],'l':'a'})
     img2 = self.imageWithProvenance({'parents':['x','a'],'l':'b'})
     img3 = self.imageWithProvenance({'parents':['b'],'l':'b'})
     img4 = self.imageWithProvenance({'parents':['c','y'],'l':'d'})
     img5 = self.imageWithProvenance({'parents':['d'],'l':'e'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3, img4, img5]
     out = repo.byParents(['x','y'])
     self.assertEqual([img2, img4], out)
Beispiel #26
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 def test_byParents(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'parents': [], 'l': 'a'})
     img2 = self.imageWithProvenance({'parents': ['x', 'a'], 'l': 'b'})
     img3 = self.imageWithProvenance({'parents': ['b'], 'l': 'b'})
     img4 = self.imageWithProvenance({'parents': ['c', 'y'], 'l': 'd'})
     img5 = self.imageWithProvenance({'parents': ['d'], 'l': 'e'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3, img4, img5]
     out = repo.byParents(['x', 'y'])
     self.assertEqual([img2, img4], out)
Beispiel #27
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def importp(filepath, dependencies=Dependencies()):
    """Add provenance in bulk from a file, such as saved by export().

    Named importp as opposed to import because the latter is a reserved word
    in Python.

    This can serve as a backup, migration tool, or for exchange.
    """
    repository = dependencies.getRepository()
    importDeps = Dependencies()
    importDeps.getConfiguration().database_url = filepath
    importRepo = JsonFile(importDeps)
    allFiles = importRepo.all()
    for pfile in allFiles:
        repository.add(pfile)
Beispiel #28
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 def test_latest(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance(
         {'added': datetime.datetime(1982, 1, 5)})
     img2 = self.imageWithProvenance(
         {'added': datetime.datetime(1982, 2, 5)})
     img3 = self.imageWithProvenance(
         {'added': datetime.datetime(1982, 3, 5)})
     img4 = self.imageWithProvenance(
         {'added': datetime.datetime(1982, 4, 5)})
     img5 = self.imageWithProvenance(
         {'added': datetime.datetime(1982, 5, 5)})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3, img4, img5]
     out = repo.latest(3)
     self.assertEqual([img5, img4, img3], out)
Beispiel #29
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 def test_Query_with_value_field(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'a': 'b'})
     img2 = self.imageWithProvenance({'color': 'red', 'a': 'd'})
     img3 = self.imageWithProvenance({'color': 'blue', 'a': 'f'})
     img4 = self.imageWithProvenance({'color': 'red', 'a': 'd'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3, img4]
     q = Mock()
     field1 = Mock()
     field1.name = 'color'
     field1.value = 'red'
     field1.all = False
     q.getFields.return_value = [field1]
     out = repo.inquire(q)
     self.assertEqual([img2, img4], out)
Beispiel #30
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 def test_Query_with_value_field(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img1 = self.imageWithProvenance({'a':'b'})
     img2 = self.imageWithProvenance({'color':'red','a':'d'})
     img3 = self.imageWithProvenance({'color':'blue','a':'f'})
     img4 = self.imageWithProvenance({'color':'red','a':'d'})
     repo.all = Mock()
     repo.all.return_value = [img1, img2, img3, img4]
     q = Mock()
     field1 = Mock()
     field1.name = 'color'
     field1.value = 'red'
     field1.all = False
     q.getFields.return_value = [field1]
     out = repo.inquire(q)
     self.assertEqual([img2, img4], out)
Beispiel #31
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 def test_Search_looks_through_multiple_fields(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     i1 = self.imageWithProvenance({'color':'red'})
     i2 = self.imageWithProvenance({'location':'redis'})
     i3 = self.imageWithProvenance({'user':'******'})
     i4 = self.imageWithProvenance({'subject':'red bastard'})
     i5 = self.imageWithProvenance({'protocol':'reddish'})
     i6 = self.imageWithProvenance({'transformation':'zoomed red'})
     i7 = self.imageWithProvenance({'technique':'redshift'})
     i8 = self.imageWithProvenance({'modality':'red'})
     repo.all = Mock()
     repo.all.return_value = [i1,i2,i3,i4,i5,i6,i7,i8]
     out = repo.search('red')
     self.assertNotIn(i1, out)
     self.assertIn(i2, out)
     self.assertIn(i3, out)
     self.assertIn(i4, out)
     self.assertIn(i5, out)
     self.assertIn(i6, out)
     self.assertIn(i7, out)
     self.assertIn(i8, out)
Beispiel #32
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 def test_Search_looks_through_multiple_fields(self):
     self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p['l']
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     i1 = self.imageWithProvenance({'color': 'red'})
     i2 = self.imageWithProvenance({'location': 'redis'})
     i3 = self.imageWithProvenance({'user': '******'})
     i4 = self.imageWithProvenance({'subject': 'red bastard'})
     i5 = self.imageWithProvenance({'protocol': 'reddish'})
     i6 = self.imageWithProvenance({'transformation': 'zoomed red'})
     i7 = self.imageWithProvenance({'technique': 'redshift'})
     i8 = self.imageWithProvenance({'modality': 'red'})
     repo.all = Mock()
     repo.all.return_value = [i1, i2, i3, i4, i5, i6, i7, i8]
     out = repo.search('red')
     self.assertNotIn(i1, out)
     self.assertIn(i2, out)
     self.assertIn(i3, out)
     self.assertIn(i4, out)
     self.assertIn(i5, out)
     self.assertIn(i6, out)
     self.assertIn(i7, out)
     self.assertIn(i8, out)
Beispiel #33
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    def test_updateApproval(self):
        from niprov.jsonfile import JsonFile
        repo = JsonFile(self.dependencies)
        img = Mock()
        img.provenance = {'fiz': 'baf', 'approval': 'notsure'}

        def assertion(img):
            self.assertEqual({
                'fiz': 'baf',
                'approval': 'excellent!'
            }, img.provenance)

        repo.byLocation = Mock()
        repo.byLocation.return_value = img
        repo.update = Mock()
        repo.update.side_effect = assertion
        repo.updateApproval('/p/f1', 'excellent!')
Beispiel #34
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 def test_Will_tell_PictureCache_to_persist_known_Snapshot(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img = self.imageWithProvenance({'location': '1', 'foo': 'baz'})
     repo.add(img)
     self.pictureCache.saveToDisk.assert_called_with(for_=img)
Beispiel #35
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 def test_Will_tell_PictureCache_to_persist_known_Snapshot(self):
     from niprov.jsonfile import JsonFile
     repo = JsonFile(self.dependencies)
     img = self.imageWithProvenance({'location':'1','foo':'baz'})
     repo.add(img)
     self.pictureCache.saveToDisk.assert_called_with(for_=img)