def test_get_samples(self):
collection = Collection(id=1, resolwe=MagicMock())
collection._samples = ['sample_1', 'sample_2']
self.assertEqual(get_samples(collection), ['sample_1', 'sample_2'])
collection_1 = Collection(id=1, resolwe=MagicMock())
collection_1._samples = ['sample_1']
collection_2 = Collection(id=2, resolwe=MagicMock())
collection_2._samples = ['sample_2']
self.assertEqual(get_samples([collection_1, collection_2]),
['sample_1', 'sample_2'])
data = Data(id=1, resolwe=MagicMock())
data._sample = 'sample_1'
self.assertEqual(get_samples(data), ['sample_1'])
data1 = Data(id=1, resolwe=MagicMock())
data1._sample = 'sample1'
data2 = Data(id=2, resolwe=MagicMock())
data2._sample = 'sample2'
self.assertEqual(get_samples([data1, data2]), ['sample1', 'sample2'])
data = Data(id=1,
resolwe=MagicMock(**{'sample.filter.return_value': None}))
data._sample = None
with self.assertRaises(TypeError):
get_samples(data)
sample = Sample(id=1, resolwe=MagicMock())
self.assertEqual(get_samples(sample), [sample])
sample_1 = Sample(id=1, resolwe=MagicMock())
sample_2 = Sample(id=3, resolwe=MagicMock())
self.assertEqual(get_samples([sample_1, sample_2]),
[sample_1, sample_2])
def test_dehydrate_resources(self):
# `Collection` is used because it is easier to use
collection = Collection(id=100, resolwe=MagicMock())
obj_1 = Collection(id=1, resolwe=MagicMock())
obj_1.id = 1 # this is overriden when initialized
self.assertEqual(collection._dehydrate_resources(obj_1), 1)
self.assertEqual(collection._dehydrate_resources([obj_1]), [1])
self.assertEqual(collection._dehydrate_resources({'key': obj_1}), {'key': 1})
self.assertEqual(collection._dehydrate_resources({'key': [obj_1]}), {'key': [1]})
def test_get_samples(self):
collection = Collection(id=1, resolwe=MagicMock())
collection._samples = ['sample_1', 'sample_2']
self.assertEqual(get_samples(collection), ['sample_1', 'sample_2'])
collection_1 = Collection(id=1, resolwe=MagicMock())
collection_1._samples = ['sample_1']
collection_2 = Collection(id=2, resolwe=MagicMock())
collection_2._samples = ['sample_2']
self.assertEqual(get_samples([collection_1, collection_2]),
['sample_1', 'sample_2'])
sample = Sample(id=1, resolwe=MagicMock())
self.assertEqual(get_samples(sample), [sample])
sample_1 = Sample(id=1, resolwe=MagicMock())
sample_2 = Sample(id=3, resolwe=MagicMock())
self.assertEqual(get_samples([sample_1, sample_2]),
[sample_1, sample_2])
def test_get_resource_collection(self):
collection = Collection(id=1, resolwe=MagicMock())
collection.id = 1 # this is overriden when initialized
self.assertEqual(get_resource_collection(collection), 1)
relation = Relation(id=1, resolwe=MagicMock())
relation._hydrated_collection = Collection(id=2, resolwe=MagicMock())
relation._hydrated_collection.id = 2 # this is overriden when initialized
self.assertEqual(get_resource_collection(relation), 2)
data = Data(id=1, resolwe=MagicMock())
data._collections = [Collection(id=3, resolwe=MagicMock())]
data._collections[0].id = 3 # this is overriden when initialized
self.assertEqual(get_resource_collection(data), 3)
sample = Sample(id=1, resolwe=MagicMock())
sample._collections = [Collection(id=4, resolwe=MagicMock())]
sample._collections[0].id = 4 # this is overriden when initialized
self.assertEqual(get_resource_collection(sample), 4)
sample = Sample(id=1, resolwe=MagicMock())
sample._collections = [
Collection(id=5, resolwe=MagicMock()),
Collection(id=6, resolwe=MagicMock())
]
sample._collections[0].id = 5 # this is overriden when initialized
sample._collections[1].id = 6 # this is overriden when initialized
self.assertEqual(get_resource_collection(sample), None)
with self.assertRaises(LookupError):
get_resource_collection(sample, fail_silently=False)
def test_get_samples(self):
collection = Collection(id=1, resolwe=MagicMock())
collection._samples = ['sample_1', 'sample_2']
self.assertEqual(get_samples(collection), ['sample_1', 'sample_2'])
collection_1 = Collection(id=1, resolwe=MagicMock())
collection_1._samples = ['sample_1']
collection_2 = Collection(id=2, resolwe=MagicMock())
collection_2._samples = ['sample_2']
self.assertEqual(get_samples([collection_1, collection_2]),
['sample_1', 'sample_2'])
data = Data(id=1, resolwe=MagicMock())
data.api(data.id).get = MagicMock(return_value={'entities': [7]})
data.resolwe.sample.get = MagicMock(return_value='sample_1')
self.assertEqual(get_samples(data), ['sample_1'])
data1 = Data(id=1, resolwe=MagicMock())
data1.api(data.id).get = MagicMock(return_value={'entities': [7]})
data1.resolwe.sample.get = MagicMock(return_value='sample1')
data2 = Data(id=2, resolwe=MagicMock())
data2.api(data.id).get = MagicMock(return_value={'entities': [8]})
data2.resolwe.sample.get = MagicMock(return_value='sample2')
self.assertEqual(get_samples([data1, data2]), ['sample1', 'sample2'])
data = Data(id=1,
resolwe=MagicMock(**{'sample.get.return_value': None}))
data._sample = None
with self.assertRaises(TypeError):
get_samples(data)
sample = Sample(id=1, resolwe=MagicMock())
self.assertEqual(get_samples(sample), [sample])
sample_1 = Sample(id=1, resolwe=MagicMock())
sample_2 = Sample(id=3, resolwe=MagicMock())
self.assertEqual(get_samples([sample_1, sample_2]),
[sample_1, sample_2])
def test_dehydrate_collections(self, resolwe_mock):
resolwe_mock.configure_mock(**{'_get_process.return_value': {'slug': 'some:prc:slug:'},
'_process_inputs.return_value': {}})
resolwe_mock.collection = MagicMock()
resolwe_mock.api = MagicMock(**{'process.get.return_value': self.process_json,
'data.post.return_value': {}})
collection = Collection(id=1, resolwe=MagicMock())
collection.id = 1 # this is overriden when initialized
Resolwe.run(resolwe_mock, collections=[collection])
resolwe_mock.api.data.post.assert_called_once_with(
{'process': 'some:prc:slug:', 'input': {}, 'collections': [1]})
def setUp(self):
self.res = resdk.Resolwe(EMAIL, PASSW, URL)
self.reads = os.path.abspath(
os.path.normpath(
os.path.dirname(__file__) + "./../files/example.fastq"))
self.data = self.res.run(slug='upload-fastq-single',
input={'src': [self.reads]})
wait_for_update(self.data, maxtime=20, step=2)
self.contributor = self.data.contributor
# Make collection and add self.data to it.
json_data = self.res.api.collection.post(
{u'name': 'testing_collection'})
self.collection = Collection(model_data=json_data, resolwe=self.res)
def setUp(self):
self.res = resdk.Resolwe(EMAIL, PASSW, URL)
self.reads = os.path.abspath(
os.path.normpath(
os.path.dirname(__file__) + "./../files/example.fastq"))
self.yaml_path = os.path.abspath(
os.path.normpath(
os.path.dirname(__file__) + "./../files/custom_process.yaml"))
self.tool1_path = os.path.abspath(
os.path.normpath(os.path.dirname(__file__) + "./../files/sum.py"))
# # Make a collection:
colllection_json = self.res.api.collection.post(
{u'name': 'test_collection'})
self.collection = Collection(model_data=colllection_json,
resolwe=self.res)
self.result = None
def test_dehydrate_collection(self, resolwe_mock):
resolwe_mock._get_process.return_value = Process(
resolwe=MagicMock(), slug="process-slug"
)
resolwe_mock._process_inputs.return_value = {}
resolwe_mock.api = MagicMock(**{"data.post.return_value": {}})
Resolwe.run(
self=resolwe_mock,
slug="process-slug",
collection=Collection(id=1, resolwe=MagicMock()),
)
resolwe_mock.api.data.post.assert_called_once_with(
{
"process": {"slug": "process-slug"},
"input": {},
"collection": {"id": 1},
}
)
def test_dehydrate_collection(self, resolwe_mock):
resolwe_mock._get_process.return_value = Process(resolwe=MagicMock(),
slug='process-slug')
resolwe_mock._process_inputs.return_value = {}
resolwe_mock.api = MagicMock(**{'data.post.return_value': {}})
Resolwe.run(
self=resolwe_mock,
slug='process-slug',
collection=Collection(id=1, resolwe=MagicMock()),
)
resolwe_mock.api.data.post.assert_called_once_with({
'process': {
'slug': 'process-slug'
},
'input': {},
'collection': {
'id': 1
},
})
def test_get_collection_id(self):
collection = Collection(id=1, resolwe=MagicMock())
collection.id = 1 # this is overriden when initialized
self.assertEqual(get_collection_id(collection), 1)
self.assertEqual(get_collection_id(2), 2)
header = next(sample_reader)
for row in sample_reader:
samples[row[0]] = {col: '' for col in header}
for i, column in enumerate(row):
if i == 0:
continue # skip sample name
samples[row[0]] [header[i]] = column
for s in samples:
collection_name = samples[s]['COLLECTION']
try:
collection = res.collection.get(name=collection_name)
except LookupError:
collection = Collection(resolwe=res)
collection.name = collection_name
collection.save()
if samples[s]['PAIRED'] == '0':
src = samples[s]['FASTQ_R1'].split(",")
print('Uploading data for sample: {}'.format(s))
reads = res.run('upload-fastq-single',
input={'src': src},
collections=[collection.id])
elif samples[s]['PAIRED'] == '1':
src1 = samples[s]['FASTQ_R1'].strip(',').split(',')
src2 = samples[s]['FASTQ_R2'].strip(',').split(',')
print('Uploading data for sample: {}'.format(s))