class MongoRepoTests(DependencyInjectionTestBase):
def setUp(self):
super(MongoRepoTests, self).setUp()
self.pictureCache.getBytes.return_value = None
self.db = Mock()
self.db.provenance.find_one.return_value = {}
self.db.provenance.find.return_value = {}
self.pymongo = None
def setupRepo(self):
from niprov.mongo import MongoRepository
with patch('niprov.mongo.pymongo') as self.pymongo:
self.repo = MongoRepository(dependencies=self.dependencies)
self.repo.db = self.db
def test_Connection(self):
from niprov.mongo import MongoRepository
with patch('niprov.mongo.pymongo') as pymongo:
repo = MongoRepository(dependencies=self.dependencies)
pymongo.MongoClient.assert_called_with(self.config.database_url)
self.assertEqual(pymongo.MongoClient().get_default_database(), repo.db)
def test_byLocation_returns_img_from_record_with_path(self):
self.setupRepo()
p = '/p/f1'
out = self.repo.byLocation(p)
self.db.provenance.find_one.assert_called_with({'location': p})
self.fileFactory.fromProvenance.assert_called_with(
self.db.provenance.find_one())
self.assertEqual(self.fileFactory.fromProvenance(), out)
def test_getSeries(self):
self.setupRepo()
img = Mock()
out = self.repo.getSeries(img)
self.db.provenance.find_one.assert_called_with(
{'seriesuid': img.getSeriesId()})
self.fileFactory.fromProvenance.assert_called_with(
self.db.provenance.find_one())
self.assertEqual(self.fileFactory.fromProvenance(), out)
def test_getSeries_returns_None_right_away_if_no_series_id(self):
self.setupRepo()
img = Mock()
img.getSeriesId.return_value = None
out = self.repo.getSeries(img)
assert not self.db.provenance.find_one.called
self.assertEqual(None, out)
def test_Add(self):
self.setupRepo()
img = Mock()
img.provenance = {'a': 1, 'b': 2}
self.repo.add(img)
self.db.provenance.insert_one.assert_called_with({'a': 1, 'b': 2})
def test_update(self):
self.setupRepo()
img = Mock()
img.provenance = {'a': 1, 'b': 2}
self.repo.update(img)
self.db.provenance.update.assert_called_with(
{'location': img.location.toString()}, {
'a': 1,
'b': 2
})
def test_all(self):
self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p
self.db.provenance.find.return_value = ['p1', 'p2']
self.setupRepo()
out = self.repo.all()
self.db.provenance.find.assert_called_with()
self.fileFactory.fromProvenance.assert_any_call('p1')
self.fileFactory.fromProvenance.assert_any_call('p2')
self.assertEqual(['img_p1', 'img_p2'], out)
def test_updateApproval(self):
self.setupRepo()
img = Mock()
p = '/p/f1'
newStatus = 'oh-oh'
self.repo.updateApproval(p, newStatus)
self.db.provenance.update.assert_called_with(
{'location': p}, {'$set': {
'approval': newStatus
}})
def test_latest(self):
self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p
self.db.provenance.find.return_value = Mock()
self.db.provenance.find.return_value.sort.return_value.limit.return_value = [
'px', 'py'
]
self.setupRepo()
out = self.repo.latest()
self.db.provenance.find.assert_called_with()
self.db.provenance.find().sort.assert_called_with('added', -1)
self.db.provenance.find().sort().limit.assert_called_with(20)
self.fileFactory.fromProvenance.assert_any_call('px')
self.fileFactory.fromProvenance.assert_any_call('py')
self.assertEqual(['img_px', 'img_py'], out)
def test_statistics(self):
self.db.provenance.aggregate.return_value = [
sentinel.stats,
]
self.setupRepo()
out = self.repo.statistics()
self.db.provenance.aggregate.assert_called_with([{
'$group': {
'_id': None,
'totalsize': {
'$sum': '$size'
},
'count': {
'$sum': 1
}
}
}])
self.assertEqual(sentinel.stats, out)
def test_statistics_if_no_records(self):
self.db.provenance.aggregate.return_value = []
self.setupRepo()
out = self.repo.statistics()
self.assertEqual({'count': 0}, out)
def test_byId(self):
self.setupRepo()
ID = 'abc123'
out = self.repo.byId(ID)
self.db.provenance.find_one.assert_called_with({'id': ID})
self.fileFactory.fromProvenance.assert_called_with(
self.db.provenance.find_one())
self.assertEqual(self.fileFactory.fromProvenance(), out)
def test_If_db_returns_None_should_return_None_for_byId_byLocation(self):
self.setupRepo()
self.db.provenance.find_one.return_value = None
out = self.repo.byId('abc123')
assert not self.fileFactory.fromProvenance.called
self.assertEqual(None, out)
def test_byLocations(self):
self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p
self.db.provenance.find.return_value = ['p1', 'p2']
self.setupRepo()
out = self.repo.byLocations(['l1', 'l2'])
self.db.provenance.find.assert_called_with(
{'location': {
'$in': ['l1', 'l2']
}})
self.fileFactory.fromProvenance.assert_any_call('p1')
self.fileFactory.fromProvenance.assert_any_call('p2')
self.assertEqual(['img_p1', 'img_p2'], out)
def test_byParents(self):
self.fileFactory.fromProvenance.side_effect = lambda p: 'img_' + p
self.db.provenance.find.return_value = ['p1', 'p2']
self.setupRepo()
out = self.repo.byParents(['x1', 'x2'])
self.db.provenance.find.assert_called_with(
{'parents': {
'$in': ['x1', 'x2']
}})
self.fileFactory.fromProvenance.assert_any_call('p1')
self.fileFactory.fromProvenance.assert_any_call('p2')
self.assertEqual(['img_p1', 'img_p2'], out)
def test_Obtains_optional_snapshot_data_from_cache_when_serializing(self):
self.pictureCache.getBytes.return_value = sentinel.snapbytes
with patch('niprov.mongo.bson') as bson:
bson.Binary.return_value = sentinel.snapbson
self.setupRepo()
img = Mock()
img.provenance = {'a': 1}
self.repo.add(img)
self.pictureCache.getBytes.assert_called_with(for_=img)
bson.Binary.assert_called_with(sentinel.snapbytes)
self.db.provenance.insert_one.assert_called_with({
'a':
1,
'_snapshot-data':
sentinel.snapbson
})
def test_If_no_snapshot_doesnt_add_data_field(self):
self.pictureCache.getBytes.return_value = None
with patch('niprov.mongo.bson') as bson:
self.setupRepo()
img = Mock()
img.provenance = {'a': 1}
self.repo.add(img)
assert not bson.Binary.called
self.db.provenance.insert_one.assert_called_with({'a': 1})
def test_If_snapshotdata_hands_them_to_pictureCache_on_deserializing(self):
img = Mock()
self.fileFactory.fromProvenance.return_value = img
self.setupRepo()
self.db.provenance.find_one.return_value = {'a': 3}
out = self.repo.byLocation('/p/f1')
assert not self.pictureCache.keep.called
self.db.provenance.find_one.return_value = {
'a': 3,
'_snapshot-data': 'y7yUyS'
}
out = self.repo.byLocation('/p/f1')
self.pictureCache.keep.assert_called_with('y7yUyS', for_=img)
def test_Query(self):
self.db.provenance.find.return_value = ['record1']
self.setupRepo()
q = Mock()
field1 = Mock()
field1.name = 'color'
field1.value = 'red'
field1.all = False
q.getFields.return_value = [field1]
out = self.repo.inquire(q)
self.db.provenance.find.assert_called_with({'color': 'red'})
self.fileFactory.fromProvenance.assert_called_with('record1')
def test_Ensures_text_index_for_search(self):
self.setupRepo()
self.repo.search('')
searchfields = [
'location', 'user', 'subject', 'project', 'protocol',
'transformation', 'technique', 'modality'
]
indexspec = [(field, 'text') for field in searchfields]
self.db.provenance.create_index.assert_called_with(indexspec,
name='textsearch')
def test_Search(self):
self.db.provenance.find.return_value = ['r1', 'r2']
self.setupRepo()
self.repo.search('xyz')
self.db.provenance.find.assert_called_with(
{'$text': {
'$search': 'xyz'
}})
self.fileFactory.fromProvenance.assert_any_call('r1')
self.fileFactory.fromProvenance.assert_any_call('r2')
def test_Query_for_ALL_field(self):
self.db.provenance.distinct.return_value = ['r1', 'r2']
self.setupRepo()
q = Mock()
field1 = Mock()
field1.name = 'color'
field1.all = True
q.getFields.return_value = [field1]
out = self.repo.inquire(q)
self.db.provenance.distinct.assert_called_with('color')
assert not self.fileFactory.fromProvenance.called
def test_Connection(self):
from niprov.mongo import MongoRepository
with patch('niprov.mongo.pymongo') as pymongo:
repo = MongoRepository(dependencies=self.dependencies)
pymongo.MongoClient.assert_called_with(self.config.database_url)
self.assertEqual(pymongo.MongoClient().get_default_database(), repo.db)
class MongoRepoTests(DependencyInjectionTestBase):
def setUp(self):
super(MongoRepoTests, self).setUp()
self.pictureCache.getBytes.return_value = None
self.db = Mock()
self.db.provenance.find_one.return_value = {}
self.db.provenance.find.return_value = {}
self.pymongo = None
def setupRepo(self):
from niprov.mongo import MongoRepository
with patch('niprov.mongo.pymongo') as self.pymongo:
self.repo = MongoRepository(dependencies=self.dependencies)
self.repo.db = self.db
def test_Connection(self):
from niprov.mongo import MongoRepository
with patch('niprov.mongo.pymongo') as pymongo:
repo = MongoRepository(dependencies=self.dependencies)
pymongo.MongoClient.assert_called_with(self.config.database_url)
self.assertEqual(pymongo.MongoClient().get_default_database(), repo.db)
def test_byLocation_returns_img_from_record_with_path(self):
self.setupRepo()
p = '/p/f1'
out = self.repo.byLocation(p)
self.db.provenance.find_one.assert_called_with({'location':p})
self.fileFactory.fromProvenance.assert_called_with(
self.db.provenance.find_one())
self.assertEqual(self.fileFactory.fromProvenance(), out)
def test_getSeries(self):
self.setupRepo()
img = Mock()
out = self.repo.getSeries(img)
self.db.provenance.find_one.assert_called_with(
{'seriesuid':img.getSeriesId()})
self.fileFactory.fromProvenance.assert_called_with(
self.db.provenance.find_one())
self.assertEqual(self.fileFactory.fromProvenance(), out)
def test_getSeries_returns_None_right_away_if_no_series_id(self):
self.setupRepo()
img = Mock()
img.getSeriesId.return_value = None
out = self.repo.getSeries(img)
assert not self.db.provenance.find_one.called
self.assertEqual(None, out)
def test_Add(self):
self.setupRepo()
img = Mock()
img.provenance = {'a':1, 'b':2}
self.repo.add(img)
self.db.provenance.insert_one.assert_called_with({'a':1, 'b':2})
def test_update(self):
self.setupRepo()
img = Mock()
img.provenance = {'a':1, 'b':2}
self.repo.update(img)
self.db.provenance.update.assert_called_with(
{'location':img.location.toString()}, {'a':1, 'b':2})
def test_all(self):
self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p
self.db.provenance.find.return_value = ['p1', 'p2']
self.setupRepo()
out = self.repo.all()
self.db.provenance.find.assert_called_with()
self.fileFactory.fromProvenance.assert_any_call('p1')
self.fileFactory.fromProvenance.assert_any_call('p2')
self.assertEqual(['img_p1', 'img_p2'], out)
def test_updateApproval(self):
self.setupRepo()
img = Mock()
p = '/p/f1'
newStatus = 'oh-oh'
self.repo.updateApproval(p, newStatus)
self.db.provenance.update.assert_called_with(
{'location':p}, {'$set': {'approval': newStatus}})
def test_latest(self):
self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p
self.db.provenance.find.return_value = Mock()
self.db.provenance.find.return_value.sort.return_value.limit.return_value = ['px','py']
self.setupRepo()
out = self.repo.latest()
self.db.provenance.find.assert_called_with()
self.db.provenance.find().sort.assert_called_with('added', -1)
self.db.provenance.find().sort().limit.assert_called_with(20)
self.fileFactory.fromProvenance.assert_any_call('px')
self.fileFactory.fromProvenance.assert_any_call('py')
self.assertEqual(['img_px', 'img_py'], out)
def test_statistics(self):
self.db.provenance.aggregate.return_value = [sentinel.stats,]
self.setupRepo()
out = self.repo.statistics()
self.db.provenance.aggregate.assert_called_with(
[{'$group':
{
'_id': None,
'totalsize': { '$sum': '$size' },
'count': { '$sum': 1 }
}
}])
self.assertEqual(sentinel.stats, out)
def test_statistics_if_no_records(self):
self.db.provenance.aggregate.return_value = []
self.setupRepo()
out = self.repo.statistics()
self.assertEqual({'count':0}, out)
def test_byId(self):
self.setupRepo()
ID = 'abc123'
out = self.repo.byId(ID)
self.db.provenance.find_one.assert_called_with({'id':ID})
self.fileFactory.fromProvenance.assert_called_with(
self.db.provenance.find_one())
self.assertEqual(self.fileFactory.fromProvenance(), out)
def test_If_db_returns_None_should_return_None_for_byId_byLocation(self):
self.setupRepo()
self.db.provenance.find_one.return_value = None
out = self.repo.byId('abc123')
assert not self.fileFactory.fromProvenance.called
self.assertEqual(None, out)
def test_byLocations(self):
self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p
self.db.provenance.find.return_value = ['p1', 'p2']
self.setupRepo()
out = self.repo.byLocations(['l1','l2'])
self.db.provenance.find.assert_called_with({'location':{'$in':['l1','l2']}})
self.fileFactory.fromProvenance.assert_any_call('p1')
self.fileFactory.fromProvenance.assert_any_call('p2')
self.assertEqual(['img_p1', 'img_p2'], out)
def test_byParents(self):
self.fileFactory.fromProvenance.side_effect = lambda p: 'img_'+p
self.db.provenance.find.return_value = ['p1', 'p2']
self.setupRepo()
out = self.repo.byParents(['x1','x2'])
self.db.provenance.find.assert_called_with({'parents':{'$in':['x1','x2']}})
self.fileFactory.fromProvenance.assert_any_call('p1')
self.fileFactory.fromProvenance.assert_any_call('p2')
self.assertEqual(['img_p1', 'img_p2'], out)
def test_Obtains_optional_snapshot_data_from_cache_when_serializing(self):
self.pictureCache.getBytes.return_value = sentinel.snapbytes
with patch('niprov.mongo.bson') as bson:
bson.Binary.return_value = sentinel.snapbson
self.setupRepo()
img = Mock()
img.provenance = {'a':1}
self.repo.add(img)
self.pictureCache.getBytes.assert_called_with(for_=img)
bson.Binary.assert_called_with(sentinel.snapbytes)
self.db.provenance.insert_one.assert_called_with({'a':1,
'_snapshot-data':sentinel.snapbson})
def test_If_no_snapshot_doesnt_add_data_field(self):
self.pictureCache.getBytes.return_value = None
with patch('niprov.mongo.bson') as bson:
self.setupRepo()
img = Mock()
img.provenance = {'a':1}
self.repo.add(img)
assert not bson.Binary.called
self.db.provenance.insert_one.assert_called_with({'a':1})
def test_If_snapshotdata_hands_them_to_pictureCache_on_deserializing(self):
img = Mock()
self.fileFactory.fromProvenance.return_value = img
self.setupRepo()
self.db.provenance.find_one.return_value = {'a':3}
out = self.repo.byLocation('/p/f1')
assert not self.pictureCache.keep.called
self.db.provenance.find_one.return_value = {'a':3,
'_snapshot-data':'y7yUyS'}
out = self.repo.byLocation('/p/f1')
self.pictureCache.keep.assert_called_with('y7yUyS', for_=img)
def test_Query(self):
self.db.provenance.find.return_value = ['record1']
self.setupRepo()
q = Mock()
field1 = Mock()
field1.name = 'color'
field1.value = 'red'
field1.all = False
q.getFields.return_value = [field1]
out = self.repo.inquire(q)
self.db.provenance.find.assert_called_with({'color':'red'})
self.fileFactory.fromProvenance.assert_called_with('record1')
def test_Ensures_text_index_for_search(self):
self.setupRepo()
self.repo.search('')
searchfields = ['location','user','subject','project','protocol',
'transformation','technique','modality']
indexspec = [(field, 'text') for field in searchfields]
self.db.provenance.create_index.assert_called_with(indexspec,
name='textsearch')
def test_Search(self):
self.db.provenance.find.return_value = ['r1','r2']
self.setupRepo()
self.repo.search('xyz')
self.db.provenance.find.assert_called_with({'$text':{'$search': 'xyz'}})
self.fileFactory.fromProvenance.assert_any_call('r1')
self.fileFactory.fromProvenance.assert_any_call('r2')
def test_Query_for_ALL_field(self):
self.db.provenance.distinct.return_value = ['r1','r2']
self.setupRepo()
q = Mock()
field1 = Mock()
field1.name = 'color'
field1.all = True
q.getFields.return_value = [field1]
out = self.repo.inquire(q)
self.db.provenance.distinct.assert_called_with('color')
assert not self.fileFactory.fromProvenance.called
def setupRepo(self):
from niprov.mongo import MongoRepository
with patch('niprov.mongo.pymongo') as self.pymongo:
self.repo = MongoRepository(dependencies=self.dependencies)
self.repo.db = self.db
def setupRepo(self):
from niprov.mongo import MongoRepository
with patch('niprov.mongo.pymongo') as self.pymongo:
self.repo = MongoRepository(dependencies=self.dependencies)
self.repo.db = self.db