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)
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)
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)
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)
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)
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)
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)
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)
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())
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)
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))
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)
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)
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))
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)
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)
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!')
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())
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)
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)
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'])
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'])
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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!')
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)
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)