def test_response(self) -> None:
tornado_request = HTTPRequest(url="http://example.com")
tornado_response = HTTPResponse(request=tornado_request, code=200)
expected = OpenAPIResponse(
data="",
status_code=200,
mimetype="text/html",
)
openapi_response = TornadoResponseFactory.create(tornado_response)
self.assertEqual(attr.asdict(expected), attr.asdict(openapi_response))
def test_get_metadata_for_combine_archive_file_as_biosimulations(self):
archive_filename = os.path.join(
self.FIXTURES_DIR,
'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'
)
fid = open(archive_filename, 'rb')
data = MultiDict([
('file', fid),
('omexMetadataFormat', OmexMetadataInputFormat.rdfxml.value),
])
endpoint = '/combine/metadata/biosimulations'
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
self.assertEqual(response.status_code, 200, response.json)
metadata = response.json
sed_output_specs_filename = os.path.join(
self.FIXTURES_DIR,
'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.md.json'
)
with open(sed_output_specs_filename, 'r') as file:
expected_metadata = json.load(file)
self.assertEqual(metadata, expected_metadata)
fid.close()
# validate request and response
if hasattr(self, "request_validator"):
with open(archive_filename, 'rb') as file:
file_content = file.read()
request = OpenAPIRequest(
full_url_pattern=
'https://127.0.0.1/combine/metadata/biosimulations',
method='post',
body={
'file': file_content,
'omexMetadataFormat': OmexMetadataInputFormat.rdfxml.value,
},
mimetype='multipart/form-data',
parameters=RequestParameters(),
)
result = self.request_validator.validate(request)
result.raise_for_errors()
response = OpenAPIResponse(data=json.dumps(expected_metadata),
status_code=200,
mimetype='application/json')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
def create(cls,
data,
status_code=200,
headers=None,
mimetype="application/json"):
headers = Headers(headers or {})
return OpenAPIResponse(
data=data,
status_code=status_code,
headers=headers,
mimetype=mimetype,
)
def test_validate_is_valid(self):
archive_filename = os.path.join(self.FIXTURES_DIR,
self.TEST_CASE + '.omex')
fid = open(archive_filename, 'rb')
data = MultiDict([
('file', fid),
('omexMetadataFormat', OmexMetadataInputFormat.rdfxml.value),
('omexMetadataSchema', OmexMetadataSchema.biosimulations.value),
('validateSedmlModels', False),
])
endpoint = '/combine/validate'
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
fid.close()
self.assertEqual(response.status_code, 200, response.json)
validation_report = response.json
validation_report.pop('warnings')
self.assertEqual(validation_report, {
"_type": "ValidationReport",
"status": "warnings"
})
# validate request and response
if hasattr(self, "request_validator"):
with open(archive_filename, 'rb') as file:
file_content = file.read()
request = OpenAPIRequest(
full_url_pattern='https://127.0.0.1/combine/validate',
method='post',
body={
'file': file_content,
'omexMetadataFormat': OmexMetadataInputFormat.rdfxml.value,
'omexMetadataSchema':
OmexMetadataSchema.biosimulations.value,
},
mimetype='multipart/form-data',
parameters=RequestParameters(),
)
result = self.request_validator.validate(request)
result.raise_for_errors()
response = OpenAPIResponse(data=json.dumps(validation_report),
status_code=200,
mimetype='application/json')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
def create(cls, response):
status_code = int(response.status[:3])
mimetype = ''
if response.content_type:
mimetype = response.content_type.partition(";")[0]
else:
mimetype = response.options.default_media_type
return OpenAPIResponse(
data=response.body,
status_code=status_code,
mimetype=mimetype,
)
def create_and_validate_response(request, response):
"""
Helper function to create OpenAPIResponse and validate it
:param request: OpenAPIRequest
:param response: API response
:return:
- result: result of response validation
"""
response = OpenAPIResponse(data=response.content,
status_code=response.status_code,
mimetype='application/json')
validator = ResponseValidator(spec)
result = validator.validate(request, response)
return result
def test_get_file_in_combine_archive_url(self):
archive_filename = os.path.join(
self.FIXTURES_DIR,
'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'
)
with open(archive_filename, 'rb') as file:
archive_url_content = file.read()
archive_url = 'https://archive.combine.org'
resolve_archive_response = mock.Mock(
raise_for_status=lambda: None,
content=archive_url_content,
)
endpoint = '/combine/file?url={}&location={}'.format(
urllib.parse.quote(archive_url),
urllib.parse.quote('Figure1.jpg'),
)
with mock.patch('requests.get', return_value=resolve_archive_response):
with app.app.app.test_client() as client:
response = client.get(endpoint)
self.assertEqual(response.status_code, 200, response.json)
image_filename = os.path.join(self.temp_dirname, 'image')
with open(image_filename, 'wb') as file:
file.write(response.data)
self.assertEqual(imghdr.what(image_filename), 'jpeg')
# validate request and response
if hasattr(self, "request_validator"):
request = OpenAPIRequest(
full_url_pattern='https://127.0.0.1/combine/file',
method='get',
body={
'url': archive_url,
'location': 'Figure1.jpg',
},
mimetype='multipart/form-data',
parameters=RequestParameters(url=archive_url,
location='Figure1.jpg'),
)
result = self.request_validator.validate(request)
result.raise_for_errors()
response = OpenAPIResponse(data=response.data,
status_code=200,
mimetype='image/jpeg')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
def create(cls, response):
status_code = int(response.status[:3])
mimetype = ''
if response.content_type:
mimetype = response.content_type.partition(";")[0]
else:
mimetype = response.options.default_media_type
data = get_response_text(response)
return OpenAPIResponse(
data=data,
status_code=status_code,
headers=response.headers,
mimetype=mimetype,
)
def test_get_file_in_combine_archive_error_handling(self):
endpoint = '/combine/file?url={}&location={}'.format(
urllib.parse.quote('x'),
urllib.parse.quote('Figure1.jpg'),
)
with app.app.app.test_client() as client:
response = client.get(endpoint)
self.assertEqual(response.status_code, 400, response.json)
self.assertTrue(response.json['title'].startswith(
'COMBINE/OMEX archive could not be loaded'))
if hasattr(self, "response_validator"):
request = OpenAPIRequest(
full_url_pattern='https://127.0.0.1/combine/file',
method='get',
mimetype=None,
parameters=RequestParameters(url='x', location='Figure1.jpg'),
)
response = OpenAPIResponse(data=json.dumps(response.json),
status_code=400,
mimetype='image/jpeg')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
archive_filename = os.path.join(
self.FIXTURES_DIR,
'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'
)
with open(archive_filename, 'rb') as file:
archive_url_content = file.read()
archive_url = 'https://archive.combine.org'
resolve_archive_response = mock.Mock(
raise_for_status=lambda: None,
content=archive_url_content,
)
endpoint = '/combine/file?url={}&location={}'.format(
urllib.parse.quote(archive_url),
urllib.parse.quote('undefined'),
)
with mock.patch('requests.get', return_value=resolve_archive_response):
with app.app.app.test_client() as client:
response = client.get(endpoint)
self.assertEqual(response.status_code, 400, response.json)
self.assertIn('not a valid location', response.json['title'])
def test_get_metadata_for_combine_archive_error_handling(self):
endpoint = '/combine/metadata/biosimulations'
data = MultiDict([
('omexMetadataFormat', OmexMetadataInputFormat.rdfxml.value),
])
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type='multipart/form-data')
self.assertEqual(response.status_code, 400, response.json)
self.assertIn('must be used', response.json['title'])
if hasattr(self, "response_validator"):
request = OpenAPIRequest(
full_url_pattern=
'https://127.0.0.1/combine/metadata/biosimulations',
method='post',
body={
'url': 'x',
'omexMetadataFormat': OmexMetadataInputFormat.rdfxml.value,
},
mimetype=None,
parameters=RequestParameters(),
)
response = OpenAPIResponse(data=json.dumps(response.json),
status_code=400,
mimetype='application/json')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
archive_filename = os.path.join(self.FIXTURES_DIR,
'invalid-metadata.omex')
fid = open(archive_filename, 'rb')
data = MultiDict([
('file', fid),
('omexMetadataFormat', OmexMetadataInputFormat.rdfxml.value),
])
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
self.assertEqual(response.status_code, 400, response.json)
self.assertIn('is not valid', response.json['title'])
fid.close()
def test_get_parameters_variables_for_simulation_from_file(self):
endpoint = '/sed-ml/get-parameters-variables-for-simulation'
model_filename = os.path.abspath(
os.path.join(self.FIXTURES_DIR,
'Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.xml'))
model_fid = open(model_filename, 'rb')
data = MultiDict([
('modelLanguage', 'urn:sedml:language:sbml'),
('modelingFramework', 'SBO_0000547'),
('simulationType', 'SedUniformTimeCourseSimulation'),
('simulationAlgorithm', 'KISAO_0000450'),
('modelFile', model_fid),
])
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
model_fid.close()
self.assertEqual(response.status_code, 200, response.json)
sed_doc = response.json
vars = [
data_gen['variables'][0] for data_gen in sed_doc['dataGenerators']
]
self.assertEqual(vars[0]['id'], 'time')
self.assertEqual(vars[0]['name'], 'Time')
self.assertEqual(vars[0]['symbol'], Symbol.time)
self.assertNotIn('target', vars[0])
self.assertEqual(vars[-1]['id'], 'level_species_nik')
self.assertEqual(vars[-1]['name'], 'Level of species "nik"')
self.assertNotIn('symbol', vars[-1])
vars[-1]['target']['namespaces'].sort(key=lambda ns: ns['prefix'])
self.assertEqual(
vars[-1]['target'],
{
"_type":
"SedTarget",
"value":
"/sbml:sbml/sbml:model/qual:listOfQualitativeSpecies/qual:qualitativeSpecies[@qual:id='nik']",
"namespaces": [
{
"_type":
"Namespace",
"prefix":
"qual",
"uri":
"http://www.sbml.org/sbml/level3/version1/qual/version1"
},
{
"_type": "Namespace",
"prefix": "sbml",
"uri": "http://www.sbml.org/sbml/level3/version1/core"
},
]
},
)
# validate request and response
if hasattr(self, "request_validator"):
with open(model_filename, 'rb') as file:
model_content = file.read()
request = OpenAPIRequest(
full_url_pattern='https://127.0.0.1/' + endpoint,
method='post',
body={
'modelLanguage': 'urn:sedml:language:sbml',
'modelingFramework': 'SBO_0000547',
'simulationType': 'SedUniformTimeCourseSimulation',
'simulationAlgorithm': 'KISAO_0000029',
'modelFile': model_content,
},
mimetype='multipart/form-data',
parameters=RequestParameters(),
)
result = self.request_validator.validate(request)
result.raise_for_errors()
response = OpenAPIResponse(data=json.dumps(sed_doc),
status_code=200,
mimetype='application/json')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
def test_get_manifest_for_combine_archive_error_handling(self):
endpoint = '/combine/manifest'
data = MultiDict([
('url', 'x'),
])
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
self.assertEqual(response.status_code, 400, response.json)
self.assertTrue(
response.json['title'].startswith('File could not be loaded from'))
if hasattr(self, "response_validator"):
request = OpenAPIRequest(
full_url_pattern='https://127.0.0.1/combine/manifest',
method='post',
body={
'url': 'x',
},
mimetype=None,
parameters=RequestParameters(),
)
response = OpenAPIResponse(data=json.dumps(response.json),
status_code=400,
mimetype='application/json')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
response = mock.Mock(
raise_for_status=lambda: None,
content=b'.',
)
with mock.patch('requests.get', return_value=response):
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
self.assertEqual(response.status_code, 400, response.json)
self.assertIn(
'File is not a valid manifest or a COMBINE/OMEX which contains a valid manifest',
response.json['title'])
archive_filename = os.path.join(self.FIXTURES_DIR, 'no-manifest.omex')
with open(archive_filename, 'rb') as file:
archive_url_content = file.read()
response = mock.Mock(
raise_for_status=lambda: None,
content=archive_url_content,
)
with mock.patch('requests.get', return_value=response):
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
self.assertEqual(response.status_code, 400, response.json)
self.assertIn('does not contain a manifest', response.json['title'])
archive_filename = os.path.join(self.FIXTURES_DIR, 'bad-manifest.omex')
with open(archive_filename, 'rb') as file:
archive_url_content = file.read()
response = mock.Mock(
raise_for_status=lambda: None,
content=archive_url_content,
)
with mock.patch('requests.get', return_value=response):
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
self.assertEqual(response.status_code, 400, response.json)
self.assertIn(
'File is not a valid manifest or a COMBINE/OMEX which contains a valid manifest',
response.json['title'])
def test_get_metadata_for_combine_archive_file_as_rdf_triples(self):
archive_filename = os.path.join(
self.FIXTURES_DIR,
'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'
)
fid = open(archive_filename, 'rb')
data = MultiDict([
('file', fid),
('omexMetadataFormat', OmexMetadataInputFormat.rdfxml.value),
])
endpoint = '/combine/metadata/rdf'
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
self.assertEqual(response.status_code, 200, response.json)
metadata = response.json
self.assertEqual(
metadata[0], {
'_type': 'RdfTriple',
'subject': {
'_type':
'RdfUriNode',
'value':
'http://omex-library.org/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex',
},
'predicate': {
'_type': 'RdfUriNode',
'value': 'http://purl.org/dc/elements/1.1/title',
},
'object': {
'_type':
'RdfLiteralNode',
'value':
'Morphogenesis checkpoint in budding yeast (continuous) (Ciliberto et al., Journal Cell Biology, 2003)',
}
})
fid.close()
# validate request and response
if hasattr(self, "request_validator"):
with open(archive_filename, 'rb') as file:
file_content = file.read()
request = OpenAPIRequest(
full_url_pattern='https://127.0.0.1/combine/metadata/rdf',
method='post',
body={
'file': file_content,
'omexMetadataFormat': OmexMetadataInputFormat.rdfxml.value,
},
mimetype='multipart/form-data',
parameters=RequestParameters(),
)
result = self.request_validator.validate(request)
result.raise_for_errors()
response = OpenAPIResponse(data=json.dumps(metadata),
status_code=200,
mimetype='application/json')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
def test_get_manifest_for_combine_archive_url(self):
archive_filename = os.path.join(self.FIXTURES_DIR,
self.TEST_CASE + '.omex')
with open(archive_filename, 'rb') as file:
archive_url_content = file.read()
archive_url = 'https://archive.combine.org'
data = MultiDict([
('url', archive_url),
])
response = mock.Mock(
raise_for_status=lambda: None,
content=archive_url_content,
)
endpoint = '/combine/manifest'
with mock.patch('requests.get', return_value=response):
with app.app.app.test_client() as client:
response = client.post(endpoint,
data=data,
content_type="multipart/form-data")
self.assertEqual(response.status_code, 200, response.json)
manifest = response.json
expected_manifest = {
'_type':
'CombineArchiveManifest',
'contents': [{
'_type': 'CombineArchiveManifestContent',
'format': 'http://identifiers.org/combine.specifications/sbml',
'location': {
'_type': 'CombineArchiveManifestLocation',
'path': './Caravagna2010.xml',
'value': {
'_type': 'CombineArchiveContentFile',
'filename': 'Caravagna2010.xml',
},
},
'master': False
}, {
'_type': 'CombineArchiveManifestContent',
'format':
'http://identifiers.org/combine.specifications/sed-ml',
'location': {
'_type': 'CombineArchiveManifestLocation',
'path': './BIOMD0000000912_sim.sedml',
'value': {
'_type': 'CombineArchiveContentFile',
'filename': 'BIOMD0000000912_sim.sedml',
},
},
'master': True
}, {
'_type': 'CombineArchiveManifestContent',
'format': 'http://identifiers.org/combine.specifications/omex',
'location': {
'_type': 'CombineArchiveManifestLocation',
'path': '.',
'value': {
'_type': 'CombineArchiveContentFile',
'filename': '.',
},
},
'master': False
}, {
'_type': 'CombineArchiveManifestContent',
'format':
'http://identifiers.org/combine.specifications/omex-metadata',
'location': {
'_type': 'CombineArchiveManifestLocation',
'path': 'metadata.rdf',
'value': {
'_type': 'CombineArchiveContentFile',
'filename': 'metadata.rdf',
},
},
'master': False
}]
}
self.assertEqual(manifest, expected_manifest, manifest)
# validate request and response
if hasattr(self, "request_validator"):
request = OpenAPIRequest(
full_url_pattern='https://127.0.0.1/combine/manifest',
method='post',
body={
'url': archive_url,
},
mimetype='multipart/form-data',
parameters=RequestParameters(),
)
result = self.request_validator.validate(request)
result.raise_for_errors()
response = OpenAPIResponse(data=json.dumps(expected_manifest),
status_code=200,
mimetype='application/json')
result = self.response_validator.validate(request, response)
result.raise_for_errors()
def create(cls, response):
return OpenAPIResponse(
data=response.data,
status_code=response._status_code,
mimetype=response.mimetype,
)
def create(cls, data, status_code=200, mimetype='application/json'):
return OpenAPIResponse(
data=data,
status_code=status_code,
mimetype=mimetype,
)
def _bottle_response_to_openapi_response(resp: Response) -> OpenAPIResponse:
return OpenAPIResponse(
data=resp.body,
status_code=resp.status_code,
mimetype=_get_mimetype(resp.content_type)
)
def create(cls, response):
return OpenAPIResponse(
data=response.body,
status_code=response.status_code,
mimetype=response.headers.get("content-type"),
)
