def test_bad_descriptor_input(self, resolwe_mock):
# Raise error is only one of deswcriptor/descriptor_schema is given:
message = "Set both or neither descriptor and descriptor_schema."
with six.assertRaisesRegex(self, ValueError, message):
Resolwe.run(resolwe_mock, descriptor="a")
with six.assertRaisesRegex(self, ValueError, message):
Resolwe.run(resolwe_mock, descriptor_schema="a")
def test_file_processing(self, resolwe_mock, data_mock):
resolwe_mock.api = MagicMock(
**{
'process.get.return_value': self.process_mock,
'data.post.return_value': {}
})
resolwe_mock._process_file_field = MagicMock(
side_effect=[{
'file': 'file_name1',
'file_temp': 'temp_file1'
}, {
'file': 'file_name2',
'file_temp': 'temp_file2'
}, {
'file': 'file_name3',
'file_temp': 'temp_file3'
}])
data_mock.return_value = "Data object"
Resolwe.run(resolwe_mock,
input={
"src": "/path/to/file1",
"src_list": ["/path/to/file2", "/path/to/file3"]
})
def test_bad_descriptor_input(self, resolwe_mock):
# Raise error is only one of deswcriptor/descriptor_schema is given:
message = "Set both or neither descriptor and descriptor_schema."
with six.assertRaisesRegex(self, ValueError, message):
Resolwe.run(resolwe_mock, descriptor="a")
with six.assertRaisesRegex(self, ValueError, message):
Resolwe.run(resolwe_mock, descriptor_schema="a")
def test_bad_inputs(self, resolwe_mock, os_mock):
# Good file, upload fails becouse of bad input keyword
os_mock.path.isfile.return_value = True
resolwe_mock.api = MagicMock(**{'process.get.return_value': self.process_json})
resolwe_mock._upload_file = MagicMock(return_value=None)
message = r'Field .* not in process .* input schema.'
with six.assertRaisesRegex(self, KeyError, message):
Resolwe.run(resolwe_mock, input={"bad_key": "/good/path/to/file"})
def test_file_processing(self, resolwe_mock, data_mock):
resolwe_mock.api = MagicMock(**{'process.get.return_value': self.process_json, 'data.post.return_value': {}})
resolwe_mock._process_file_field = MagicMock(side_effect=[
{'file': 'file_name1', 'file_temp': 'temp_file1'},
{'file': 'file_name2', 'file_temp': 'temp_file2'},
{'file': 'file_name3', 'file_temp': 'temp_file3'}])
data_mock.return_value = "Data object"
Resolwe.run(resolwe_mock,
input={"src": "/path/to/file1",
"src_list": ["/path/to/file2", "/path/to/file3"]})
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 test_dehydrate_collections(self, resolwe_mock):
resolwe_mock.configure_mock(
**{'_get_process.return_value': MagicMock(spec=Process, slug='some:prc:slug:'),
'_process_inputs.return_value': {}}
)
resolwe_mock.collection = MagicMock()
resolwe_mock.api = MagicMock(**{'process.get.return_value': self.process_mock,
'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 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_file_processing(self, resolwe_mock, data_mock):
resolwe_mock.api = MagicMock(
**{
"process.get.return_value": self.process_mock,
"data.post.return_value": {},
}
)
resolwe_mock._process_file_field = MagicMock(
side_effect=[
{"file": "file_name1", "file_temp": "temp_file1"},
{"file": "file_name2", "file_temp": "temp_file2"},
{"file": "file_name3", "file_temp": "temp_file3"},
]
)
data_mock.return_value = "Data object"
Resolwe.run(
resolwe_mock,
input={
"src": "/path/to/file1",
"src_list": ["/path/to/file2", "/path/to/file3"],
},
)
def test_call_with_all_args(self, resolwe_mock, os_mock, data_mock):
resolwe_mock.api = MagicMock(**{
'process.get.return_value': self.process_mock,
'data.post.return_value': {'data': 'some_data'}})
data_mock.return_value = "Data object"
data = Resolwe.run(resolwe_mock,
data_name="some_name",
descriptor="descriptor",
descriptor_schema="descriptor_schema",
collections=[1, 2, 3])
# Confirm that no files to upload in input:
self.assertEqual(resolwe_mock._upload_file.call_count, 0)
data_mock.assert_called_with(data='some_data', resolwe=resolwe_mock)
self.assertEqual(data, "Data object")
def test_call_with_all_args(self, resolwe_mock, os_mock, data_mock):
resolwe_mock.api = MagicMock(
**{
'process.get.return_value': self.process_mock,
'data.post.return_value': {
'data': 'some_data'
}
})
data_mock.return_value = "Data object"
data = Resolwe.run(resolwe_mock,
data_name="some_name",
descriptor="descriptor",
descriptor_schema="descriptor_schema",
collections=[1, 2, 3])
# Confirm that no files to upload in input:
self.assertEqual(resolwe_mock._upload_file.call_count, 0)
data_mock.assert_called_with(data='some_data', resolwe=resolwe_mock)
self.assertEqual(data, "Data object")
def test_call_with_all_args(self, resolwe_mock, os_mock, data_mock):
resolwe_mock.api = MagicMock(**{
'process.get.return_value': self.process_json,
'data.post.return_value': "model_data"})
data_mock.return_value = "Data object"
data = Resolwe.run(resolwe_mock,
data_name="some_name",
descriptor="descriptor",
descriptor_schema="descriptor_schema",
collections=[1, 2, 3],
src="123",
tools="456")
# Confirm that process was registred, tool uploaded but no files to upload in input:
self.assertEqual(resolwe_mock._register.call_count, 1)
self.assertEqual(resolwe_mock._upload_tools.call_count, 1)
self.assertEqual(resolwe_mock._upload_file.call_count, 0)
data_mock.assert_called_with(model_data='model_data', resolwe=resolwe_mock)
self.assertEqual(data, "Data object")
def test_call_with_all_args(self, resolwe_mock, os_mock, data_mock):
resolwe_mock.api = MagicMock(**{
'process.get.return_value': self.process_json,
'data.post.return_value': "model_data"})
data_mock.return_value = "Data object"
data = Resolwe.run(resolwe_mock,
data_name="some_name",
descriptor="descriptor",
descriptor_schema="descriptor_schema",
collections=[1, 2, 3],
src="123",
tools="456")
# Confirm that process was registred, tool uploaded but no files to upload in input:
self.assertEqual(resolwe_mock._register.call_count, 1)
self.assertEqual(resolwe_mock._upload_tools.call_count, 1)
self.assertEqual(resolwe_mock._upload_file.call_count, 0)
data_mock.assert_called_with(model_data='model_data', resolwe=resolwe_mock)
self.assertEqual(data, "Data object")
def test_run_process(self, resolwe_mock, data_mock):
resolwe_mock.api = MagicMock(
**{'process.get.return_value': self.process_mock})
Resolwe.run(resolwe_mock)
self.assertEqual(resolwe_mock.api.data.post.call_count, 1)
def test_process_length_gt1(self, resolwe_mock):
process_out = ['process1', 'process2']
resolwe_mock.api = MagicMock(**{'process.get.return_value': process_out})
message = "Unexpected behaviour at get process with slug .*"
with six.assertRaisesRegex(self, ValueError, message):
Resolwe.run(resolwe_mock)
def test_run_process(self, resolwe_mock, data_mock):
resolwe_mock.api = MagicMock(**{'process.get.return_value': self.process_mock})
Resolwe.run(resolwe_mock)
self.assertEqual(resolwe_mock.api.data.post.call_count, 1)
class ResolweHelper:
def __init__(self):
self.url = environ.get('RESOLWE_HOST_URL', DEFAULT_URL)
self.username = environ.get('RESOLWE_API_USERNAME', DEFAULT_USERNAME)
self.password = environ.get('RESOLWE_API_PASSWORD', DEFAULT_PASSWORD)
try:
self.res = Resolwe(self.username, self.password, self.url)
except Exception:
# TODO: raise proper exceptions and handle in GUI
raise
@staticmethod
async def check_object_status(data_object):
while True:
data_object.update()
if data_object.status == 'OK' or data_object.status == 'ER':
return True
await asyncio.sleep(0.5)
def run_process(self, slug, **kwargs):
process = self.res.get_or_run(slug, input={**kwargs})
if process.status == 'OK':
return process
# wait till task is finished
loop = asyncio.new_event_loop()
try:
loop.run_until_complete(
asyncio.wait_for(self.check_object_status(process),
timeout=60))
finally:
loop.close()
return process
def get_json(self, data_object, output_field, json_field=None):
storage_data = self.res.api.storage(
data_object.output[output_field]).get()
if json_field:
return storage_data['json'][json_field]
else:
return storage_data['json']
def get_object(self, *args, **kwargs):
return self.res.data.get(*args, **kwargs)
def list_data_objects(self, data_type):
return self.res.data.filter(type='data:table:{}'.format(data_type))
def get_descriptor_schema(self, slug):
return self.res.descriptor_schema.get(slug)
def upload_data_table(self, data_table):
if not data_table and isinstance(data_table, Table):
# raise proper warning
return
# create temp dir and pickle data.Table object
with tempfile.TemporaryDirectory() as temp_dir:
# TODO: What to do if Table is not named?
file_name = data_table.name + '.pickle'
file_path = os.path.join(temp_dir, file_name)
# save Table as pickled object
data_table.save(file_path)
# run resolwe upload process
self.res.run('data-table-upload', input={'src': file_path})
@staticmethod
def download_data_table(data_table_object):
with tempfile.TemporaryDirectory() as temp_dir:
data_table_object.download(download_dir=temp_dir)
return Table(os.path.join(temp_dir, data_table_object.name))
def test_process_length_0(self, resolwe_mock):
resolwe_mock.api = MagicMock(**{'process.get.return_value': []})
message = "Could not get process for given slug."
with six.assertRaisesRegex(self, ValueError, message):
Resolwe.run(resolwe_mock)
