def test_get_reads(self):
sample = Sample(resolwe=MagicMock(), id=42)
data1 = MagicMock(process_type='data:reads:fastq:single', id=1)
data2 = MagicMock(process_type='data:reads:fastq:single:cutadapt', id=2)
sample.data.filter = MagicMock(return_value=[data2, data1])
self.assertEqual(sample.get_reads(), data2)
def test_update_descriptor(self, sample_mock):
sample_mock.configure_mock(id=42, api=MagicMock())
Sample.update_descriptor(sample_mock, {'field': 'value'})
sample_mock.api(42).patch.assert_called_once_with(
{u'descriptor': {
'field': 'value'
}})
def test_get_reads(self):
sample = Sample(resolwe=MagicMock(), id=42)
data1 = MagicMock(process_type="data:reads:fastq:single", id=1)
data2 = MagicMock(process_type="data:reads:fastq:single:cutadapt", id=2)
sample.data.filter = MagicMock(return_value=[data2, data1])
self.assertEqual(sample.get_reads(), data2)
def test_confirm_is_annotated(self, sample_mock):
sample_mock.configure_mock(endpoint='sample',
id=42,
api=MagicMock(),
logger=MagicMock())
Sample.confirm_is_annotated(sample_mock)
sample_mock.api(42).patch.assert_called_once_with(
{'descriptor_completed': True})
def test_confirm_is_annotated(self, sample_mock):
sample_mock.configure_mock(endpoint='anything but presample')
with self.assertRaises(NotImplementedError):
Sample.confirm_is_annotated(sample_mock)
sample_mock.configure_mock(endpoint='presample', id=42,
api=MagicMock(), logger=MagicMock())
Sample.confirm_is_annotated(sample_mock)
sample_mock.api(42).patch.assert_called_once_with({'presample': False})
def test_data(self):
resolwe_mock = MagicMock(**{'data.filter.return_value': ['data_1', 'data_2', 'data_3']})
sample = Sample(id=1, resolwe=resolwe_mock)
self.assertEqual(sample.data, ['data_1', 'data_2', 'data_3'])
# cache is cleared at update
sample.data = MagicMock()
sample.update()
self.assertEqual(sample.data.clear_cache.call_count, 1) # pylint: disable=no-member
def test_collections(self):
resolwe_mock = MagicMock(
**{'collection.filter.return_value': ['collection_1', 'collection_2']})
sample = Sample(id=1, resolwe=resolwe_mock)
self.assertEqual(sample.collections, ['collection_1', 'collection_2'])
# cache is cleared at update
sample.collections = MagicMock()
sample.update()
self.assertEqual(sample.collections.clear_cache.call_count, 1)
def test_descriptor_schema(self):
sample = Sample(id=1, resolwe=MagicMock())
sample._descriptor_schema = 1
# test getting descriptor schema attribute
sample.resolwe.descriptor_schema.get = MagicMock(return_value='descriptor_schema')
self.assertEqual(sample.descriptor_schema, 'descriptor_schema')
_, get_kwargs = sample.resolwe.descriptor_schema.get.call_args
self.assertEqual(get_kwargs['id'], 1)
# descriptor schema is not set
sample._descriptor_schema = None
self.assertEqual(sample.descriptor_schema, None)
# cache is cleared at update
sample._hydrated_descriptor_schema = 'descriptor_schema'
sample.update()
self.assertEqual(sample._hydrated_descriptor_schema, None)
# new collection
sample = Sample(resolwe=MagicMock())
sample.descriptor_schema = 'my-schema'
self.assertEqual(sample._descriptor_schema, 'my-schema')
sample.resolwe.descriptor_schema.get = MagicMock(return_value='descriptor_schema')
self.assertEqual(sample.descriptor_schema, 'descriptor_schema')
_, get_kwargs = sample.resolwe.descriptor_schema.get.call_args
self.assertEqual(get_kwargs['slug'], 'my-schema')
# hidrated descriptor schema
descriptor_schema = {
"slug": "test-schema",
"name": "Test schema",
"version": "1.0.0",
"schema": [
{
"default": "56G",
"type": "basic:string:",
"name": "description",
"label": "Object description"
}
],
"id": 1,
}
sample = Sample(id=1, descriptor_schema=descriptor_schema, resolwe=MagicMock())
self.assertTrue(isinstance(sample.descriptor_schema, DescriptorSchema))
# pylint: disable=no-member
self.assertEqual(sample.descriptor_schema.slug, 'test-schema')
def test_data(self):
sample = Sample(id=1, resolwe=MagicMock())
# test getting data attribute
sample.resolwe.data.filter = MagicMock(return_value=['data_1', 'data_2', 'data_3'])
self.assertEqual(sample.data, ['data_1', 'data_2', 'data_3'])
# test caching data attribute
self.assertEqual(sample.data, ['data_1', 'data_2', 'data_3'])
self.assertEqual(sample.resolwe.data.filter.call_count, 1)
# cache is cleared at update
sample._data = ['data']
sample.update()
self.assertEqual(sample._data, None)
# raising error if sample is not saved
sample.id = None
with self.assertRaises(ValueError):
_ = sample.data
def test_descriptor_schema(self):
# hidrated descriptor schema
descriptor_schema = {
"slug": "test-schema",
"name": "Test schema",
"version": "1.0.0",
"schema": [
{
"default": "56G",
"type": "basic:string:",
"name": "description",
"label": "Object description",
}
],
"id": 1,
}
sample = Sample(id=1, descriptor_schema=descriptor_schema, resolwe=MagicMock())
self.assertTrue(isinstance(sample.descriptor_schema, DescriptorSchema))
self.assertEqual(sample.descriptor_schema.slug, "test-schema")
def test_sample(self):
data = Data(id=1, resolwe=MagicMock())
data.api(data.id).get = MagicMock(return_value={'entities': [5]})
data.resolwe.sample.get = MagicMock(
return_value=Sample(data.resolwe, **{'id': 5, 'name': 'XYZ'}))
self.assertEqual(data.sample.id, 5)
self.assertEqual(data.sample.name, 'XYZ')
# test caching
self.assertEqual(data.sample.id, 5)
self.assertEqual(data.resolwe.sample.get.call_count, 1)
# cache is cleared at update
data.update()
self.assertEqual(data._sample, None)
# raising error if data object is not saved
data.id = None
with self.assertRaises(ValueError):
_ = data.sample
def test_collections(self):
sample = Sample(id=1, resolwe=MagicMock())
sample._original_values = {'collections': [1, 2, 3]}
# test getting data attribute
sample.resolwe.collection.filter = MagicMock(
return_value=['collection_1', 'collection_2', 'collection_3'])
self.assertEqual(sample.collections, ['collection_1', 'collection_2', 'collection_3'])
# test caching data attribute
self.assertEqual(sample.collections, ['collection_1', 'collection_2', 'collection_3'])
self.assertEqual(sample.resolwe.collection.filter.call_count, 1)
# cache is cleared at update
sample._collections = ['collection']
sample.update()
self.assertEqual(sample._collections, None)
# raising error if sample is not saved
sample.id = None
with self.assertRaises(ValueError):
_ = sample.collections
def test_data(self):
sample = Sample(id=1, resolwe=MagicMock())
# test getting data attribute
sample.resolwe.data.filter = MagicMock(return_value=['data_1', 'data_2', 'data_3'])
self.assertEqual(sample.data, ['data_1', 'data_2', 'data_3'])
# test caching data attribute
self.assertEqual(sample.data, ['data_1', 'data_2', 'data_3'])
self.assertEqual(sample.resolwe.data.filter.call_count, 1)
# cache is cleared at update
sample._data = ['data']
sample.update()
self.assertEqual(sample._data, None)
# raising error if sample is not saved
sample.id = None
with self.assertRaises(ValueError):
_ = sample.data
def test_collections(self):
sample = Sample(id=1, resolwe=MagicMock())
sample._original_values = {'collections': [1, 2, 3]}
# test getting data attribute
sample.resolwe.collection.filter = MagicMock(
return_value=['collection_1', 'collection_2', 'collection_3'])
self.assertEqual(sample.collections, ['collection_1', 'collection_2', 'collection_3'])
# test caching data attribute
self.assertEqual(sample.collections, ['collection_1', 'collection_2', 'collection_3'])
self.assertEqual(sample.resolwe.collection.filter.call_count, 1)
# cache is cleared at update
sample._collections = ['collection']
sample.update()
self.assertEqual(sample._collections, None)
# raising error if sample is not saved
sample.id = None
with self.assertRaises(ValueError):
_ = sample.collections
def test_descriptor_schema(self):
sample = Sample(id=1, resolwe=MagicMock())
sample._descriptor_schema = 1
# test getting descriptor schema attribute
sample.resolwe.descriptor_schema.get = MagicMock(return_value='descriptor_schema')
self.assertEqual(sample.descriptor_schema, 'descriptor_schema')
_, get_kwargs = sample.resolwe.descriptor_schema.get.call_args
self.assertEqual(get_kwargs['id'], 1)
# descriptor schema is not set
sample._descriptor_schema = None
self.assertEqual(sample.descriptor_schema, None)
# cache is cleared at update
sample._hydrated_descriptor_schema = 'descriptor_schema'
sample.update()
self.assertEqual(sample._hydrated_descriptor_schema, None)
# new collection
sample = Sample(resolwe=MagicMock())
sample.descriptor_schema = 'my-schema'
self.assertEqual(sample._descriptor_schema, 'my-schema')
sample.resolwe.descriptor_schema.get = MagicMock(return_value='descriptor_schema')
self.assertEqual(sample.descriptor_schema, 'descriptor_schema')
_, get_kwargs = sample.resolwe.descriptor_schema.get.call_args
self.assertEqual(get_kwargs['slug'], 'my-schema')
# hidrated descriptor schema
descriptor_schema = {
"slug": "test-schema",
"name": "Test schema",
"version": "1.0.0",
"schema": [
{
"default": "56G",
"type": "basic:string:",
"name": "description",
"label": "Object description"
}
],
"id": 1,
}
sample = Sample(id=1, descriptor_schema=descriptor_schema, resolwe=MagicMock())
self.assertTrue(isinstance(sample.descriptor_schema, DescriptorSchema))
# pylint: disable=no-member
self.assertEqual(sample.descriptor_schema.slug, 'test-schema')
def test_confirm_is_annotated(self, sample_mock):
sample_mock.configure_mock(endpoint='sample', id=42, api=MagicMock(), logger=MagicMock())
Sample.confirm_is_annotated(sample_mock)
sample_mock.api(42).patch.assert_called_once_with({'descriptor_completed': True})
def test_update_descriptor(self, sample_mock):
sample_mock.configure_mock(id=42, api=MagicMock())
Sample.update_descriptor(sample_mock, {'field': 'value'})
sample_mock.api(42).patch.assert_called_once_with({'descriptor': {'field': 'value'}})
def test_sample_print_annotation(self, sample_mock):
with self.assertRaises(NotImplementedError):
Sample.print_annotation(sample_mock)
def test_sample_init(self, sample_mock):
sample_mock.configure_mock(endpoint="fake_endpoint")
Sample.__init__(sample_mock, id=1, resolwe=MagicMock())
def test_sample_print_annotation(self, sample_mock):
with self.assertRaises(NotImplementedError):
Sample.print_annotation(sample_mock)