本文整理汇总了Python中resdk.resolwe.Resolwe类的典型用法代码示例。如果您正苦于以下问题:Python Resolwe类的具体用法?Python Resolwe怎么用?Python Resolwe使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了Resolwe类的15个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_empty_file_list
def test_empty_file_list(self, resolwe_mock, os_mock):
resolwe_mock.configure_mock(**self.config)
os_mock.path.isfile.return_value = True
Resolwe.download_files(resolwe_mock, [])
resolwe_mock.logger.info.assert_called_once_with("No files to download.")
示例2: test_log_if_returncode_gt1
def test_log_if_returncode_gt1(self, subprocess_mock):
fake_subprocess = MagicMock(returncode=2, **{'communicate.return_value': ['Standard output...', 'b']})
subprocess_mock.Popen = MagicMock(return_value=fake_subprocess)
Resolwe._upload_tools(self.resolwe_mock, self.tools)
self.assertEqual(self.resolwe_mock.logger.warning.call_count, 1)
示例3: test_init
def test_init(self, resolwe_mock, resauth_mock, slumber_mock, resolwe_api_mock,
resolwe_querry_mock, log_mock):
Resolwe.__init__(resolwe_mock, 'a', 'b', 'http://some/url')
# There are ten instances of ResolweQuery in init: data, process, sample, relations,
# collection, descriptorschema, user, gorup, feature and mapping.
self.assertEqual(resolwe_querry_mock.call_count, 10)
self.assertEqual(log_mock.getLogger.call_count, 1)
示例4: test_bad_descriptor_input
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")
示例5: test_invalid_file_name
def test_invalid_file_name(self, resolwe_mock, os_mock):
os_mock.configure_mock(**{'path.isfile.return_value': False})
message = r"File .* not found."
with six.assertRaisesRegex(self, ValueError, message):
Resolwe._process_file_field(resolwe_mock, "/bad/path/to/file")
self.assertEqual(resolwe_mock._upload_file.call_count, 0)
示例6: test_upload_file
def test_upload_file(self, resolwe_mock, sys_mock, requests_mock):
# Example file:
fn = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'files', 'example.fastq')
resolwe_mock.url = 'http://some/url'
resolwe_mock.auth = MagicMock()
# Supress upload progress messages:
sys_mock.sys.stdout.write = MagicMock()
sys_mock.sys.stdout.flush = MagicMock()
# Immitate response form server - always status 200
requests_response = {'files': [{'temp': 'fake_name'}]}
requests_mock.post.return_value = MagicMock(status_code=200, **{'json.return_value': requests_response})
resolwe = Resolwe._upload_file(resolwe_mock, fn)
self.assertEqual(resolwe, 'fake_name')
# Immitate response form server - always status 400
requests_mock.post.return_value = MagicMock(status_code=400)
resolwe = Resolwe._upload_file(resolwe_mock, fn)
self.assertIsNone(resolwe)
# Immitate response form server - one status 400, but other 200
requests_response = {'files': [{'temp': 'fake_name'}]}
response_ok = MagicMock(status_code=200, **{'json.return_value': requests_response})
response_fails = MagicMock(status_code=400)
requests_mock.post.side_effect = [response_ok, response_fails, response_ok, response_ok]
resolwe = Resolwe._upload_file(resolwe_mock, fn)
self.assertEqual(resolwe, 'fake_name')
示例7: test_init
def test_init(self, resolwe_mock, resauth_mock, slumber_mock, resolwe_querry_mock, log_mock):
Resolwe.__init__(resolwe_mock, 'a', 'b', 'http://some/url')
self.assertEqual(resauth_mock.call_count, 1)
self.assertEqual(slumber_mock.API.call_count, 1)
# There are four instances of ResolweQuerry in init: data, process, sample and collection:
self.assertEqual(resolwe_querry_mock.call_count, 4)
self.assertEqual(log_mock.getLogger.call_count, 1)
示例8: test_print_upload_processes
def test_print_upload_processes(self, resolwe_mock, sys_mock):
# Check output is correct
resolwe_mock.processes.return_value = PROCESS_SAMPLE
sys_mock.stdout.write = MagicMock()
Resolwe.print_upload_processes(resolwe_mock)
sys_mock.stdout.write.assert_called_with('Upload NGS reads\n')
示例9: test_completely_new_process
def test_completely_new_process(self):
"""If process with given slug does not exist, process.filter will return empty list"""
self.resolwe_mock.process.filter.return_value = []
Resolwe._register(self.resolwe_mock, self.yaml_file, "alignment-bowtie")
self.assertEqual(self.resolwe_mock.api.process.post.call_count, 1)
self.assertEqual(self.resolwe_mock._version_int_to_string.call_count, 0)
示例10: test_fail_if_bad_dir
def test_fail_if_bad_dir(self, resolwe_mock, os_mock):
resolwe_mock.configure_mock(**self.config)
os_mock.path.isfile.return_value = False
message = "Download directory does not exist: .*"
with six.assertRaisesRegex(self, ValueError, message):
Resolwe.download_files(resolwe_mock, self.file_list)
示例11: test_raise_if_returncode_1
def test_raise_if_returncode_1(self, subprocess_mock):
fake_subprocess = MagicMock(returncode=1, **{'communicate.return_value': ['Standard output...', 'b']})
subprocess_mock.Popen = MagicMock(return_value=fake_subprocess)
message = r"Tools file not found: .*"
with six.assertRaisesRegex(self, ValueError, message):
Resolwe._upload_tools(self.resolwe_mock, self.tools)
示例12: test_bad_inputs
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"})
示例13: test_if_upload_fails
def test_if_upload_fails(self, resolwe_mock, os_mock):
# Good file, upload fails
os_mock.configure_mock(**{'path.isfile.return_value': True})
resolwe_mock._upload_file = MagicMock(return_value=None)
message = r'Upload failed for .*'
with six.assertRaisesRegex(self, Exception, message):
Resolwe._process_file_field(resolwe_mock, "/good/path/to/file")
self.assertEqual(resolwe_mock._upload_file.call_count, 1)
示例14: test_bad_inputs
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
process = self.process_mock
resolwe_mock._upload_file = MagicMock(return_value=None)
message = r'Field .* not in process .* input schema.'
with self.assertRaisesRegex(ValidationError, message):
Resolwe._process_inputs(resolwe_mock, {"bad_key": "/good/path/to/file"}, process)
示例15: test_wrap_list
def test_wrap_list(self, resolwe_mock):
process = self.process_mock
Resolwe._process_inputs(resolwe_mock, {"src_list": ["/path/to/file"]}, process)
resolwe_mock._process_file_field.assert_called_once_with('/path/to/file')
resolwe_mock.reset_mock()
Resolwe._process_inputs(resolwe_mock, {"src_list": "/path/to/file"}, process)
resolwe_mock._process_file_field.assert_called_once_with('/path/to/file')