def test_get_single_id(self):
"""Tests the retrieval of information for one ID"""
# Normal query
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1")
assert len(res[0]['result']) == 8196
# Query with limit
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1",
options={'limit': 2042})
assert len(res[0]['result']) == 2042
# Query with skip
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1",
options={'skip': 3000})
assert len(res[0]['result']) == 5196
# Query with limit and skip
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1",
options={'limit': 2000, 'skip': 42})
assert len(res[0]['result']) == 2000
def test_get_single_id(self):
"""Tests the retrieval of information for one ID"""
# Normal query
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1')
assert len(res[0]['result']) == 8140
# Query with limit
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1',
options={'limit': 2042})
assert len(res[0]['result']) == 2042
# Query with skip
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1',
options={'skip': 3000})
assert len(res[0]['result']) == 5140
# Query with limit and skip
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1',
options={'limit': 2000, 'skip': 42})
assert len(res[0]['result']) == 2000
def test_url_creation(self):
"""Tests the correct creation of the url"""
# Normal query
res = get(session=self._session,
host=self._host,
version=self._version,
species=self._species,
category='feature',
subcategory='gene',
resource='snp',
query_id='BRCA1',
options={'limit': 200})
assert len(res[0]['result']) == 200
# Query with a dict option
res = get(session=self._session,
host=self._host,
version=self._version,
species=self._species,
category='feature',
subcategory='gene',
resource='snp',
query_id='BRCA1',
options={
'limit': 200,
'include': ['chromosome', 'start']
})
assert len(res[0]['result']) == 200
def test_url_creation(self):
"""Tests the correct creation of the url"""
# Normal query
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1', options={'limit': 200})
assert len(res[0]['result']) == 200
# Query with a dict option
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1',
options={'limit': 200, 'include': ['chromosome', 'start']})
assert len(res[0]['result']) == 200
def test_get_multiple_ids(self):
"""Tests the retrieval of information for multiple IDs"""
# Normal query with string ids
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1,BRCA2,LDLR')
assert len(res) == 3
assert len(res[0]['result']) == 8140
assert len(res[1]['result']) == 10419
assert len(res[2]['result']) == 4108
# Normal query with list ids
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id=['BRCA1', 'BRCA2', 'LDLR'])
assert len(res) == 3
assert len(res[0]['result']) == 8140
assert len(res[1]['result']) == 10419
assert len(res[2]['result']) == 4108
# Query with limit
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1,BRCA2,LDLR',
options={'limit': 8000})
assert len(res) == 3
assert len(res[0]['result']) == 8000
assert len(res[1]['result']) == 8000
assert len(res[2]['result']) == 4108
# Query with skip
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1,BRCA2,LDLR',
options={'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4140
assert len(res[1]['result']) == 6419
assert len(res[2]['result']) == 108
# Query with limit and skip
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1,BRCA2,LDLR',
options={'limit': 6000, 'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4140
assert len(res[1]['result']) == 6000
assert len(res[2]['result']) == 108
def test_multiple_threads(self):
"""Tests the retrieval of information with multiple threads"""
# Modifying the number of ids needed for multithreading
get.__globals__['_CALL_BATCH_SIZE'] = 2
# Normal query
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1,BRCA2,LDLR')
assert len(res) == 3
assert len(res[0]['result']) == 8140
assert len(res[1]['result']) == 10419
assert len(res[2]['result']) == 4108
# Query with limit
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1,BRCA2,LDLR',
options={'limit': 8000})
assert len(res) == 3
assert len(res[0]['result']) == 8000
assert len(res[1]['result']) == 8000
assert len(res[2]['result']) == 4108
# Query with skip
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1,BRCA2,LDLR',
options={'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4140
assert len(res[1]['result']) == 6419
assert len(res[2]['result']) == 108
# Query with limit and skip
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id='BRCA1,BRCA2,LDLR',
options={'limit': 6000, 'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4140
assert len(res[1]['result']) == 6000
assert len(res[2]['result']) == 108
def test_multiple_threads(self):
# Modifying the number of ids needed for multithreading
get.__globals__['_CALL_BATCH_SIZE'] = 2
# Normal query
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1,BRCA2,LDLR")
assert len(res) == 3
assert len(res[0]['result']) == 8196
assert len(res[1]['result']) == 10519
assert len(res[2]['result']) == 4113
# Query with limit
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1,BRCA2,LDLR",
options={'limit': 8000})
assert len(res) == 3
assert len(res[0]['result']) == 8000
assert len(res[1]['result']) == 8000
assert len(res[2]['result']) == 4113
# Query with skip
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1,BRCA2,LDLR",
options={'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4196
assert len(res[1]['result']) == 6519
assert len(res[2]['result']) == 113
# Query with limit and skip
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1,BRCA2,LDLR",
options={'limit': 6000, 'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4196
assert len(res[1]['result']) == 6000
assert len(res[2]['result']) == 113
def get_help(self, method_name=None, show_params=False, **options):
# Getting swagger documentation
response = get(session=self._session,
host=self._configuration.host,
version='swagger.json',
species=None,
category=None,
subcategory=None,
resource=None,
options=options)
sys.stdout.write(self.__class__.__name__ + '\n')
# Getting class methods
methods = [
func for func in dir(self)
if callable(getattr(self, func)) and not func.startswith('_')
]
text = '{indent}{bullet} {name}: {desc}\n'
for method in methods:
if method_name is not None and method_name != method:
continue
# Getting method info
method_swag = (method[4:] if method.startswith('get_') else method)
path_info = [
response['paths'][path] for path in response['paths']
if self._category in path and self._subcategory in path
and method_swag in path
]
if not path_info:
continue
if 'summary' not in path_info[0]['get']:
continue
desc = path_info[0]['get']['summary']
desc = desc.replace('http://bioinfo.hpc.cam.ac.uk/cellbase',
self._configuration.host)
sys.stdout.write(
text.format(indent=' ' * 4, bullet='-', name=method,
desc=desc))
# Getting method parameters
if not show_params:
continue
for param in path_info[0]['get']['parameters']:
if param['name'] in ['version', 'species', 'Output format']:
continue
desc = param['description'] if 'description' in param else '-'
desc = desc.replace('http://bioinfo.hpc.cam.ac.uk/cellbase',
self._configuration.host)
sys.stdout.write(
text.format(indent=' ' * 8,
bullet='*',
name=param['name'],
desc=desc))
def test_get_multiple_ids(self):
"""Tests the retrieval of information for multiple ID"""
# Normal query
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1,BRCA2,LDLR")
assert len(res) == 3
assert len(res[0]['result']) == 8196
assert len(res[1]['result']) == 10519
assert len(res[2]['result']) == 4113
# Query with limit
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1,BRCA2,LDLR",
options={'limit': 8000})
assert len(res) == 3
assert len(res[0]['result']) == 8000
assert len(res[1]['result']) == 8000
assert len(res[2]['result']) == 4113
# Query with skip
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1,BRCA2,LDLR",
options={'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4196
assert len(res[1]['result']) == 6519
assert len(res[2]['result']) == 113
# Query with limit and skip
res = get(host=self._host, port=self._port, version=self._version,
species=self._species, category="feature", subcategory="gene",
resource="snp", query_id="BRCA1,BRCA2,LDLR",
options={'limit': 6000, 'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4196
assert len(res[1]['result']) == 6000
assert len(res[2]['result']) == 113
def test_get_multiple_ids_with_list_ids(self):
"""Normal query with list ids"""
res = get(session=self._session,
host=self._host,
version=self._version,
species=self._species,
category='feature',
subcategory='gene',
resource='snp',
query_id=['BRCA1', 'BRCA2', 'LDLR'])
self.check_counts(res)
def get(self, category, subcategory, resource, query_id=None, **options):
"""Creates the URL for querying the REST service"""
response = get(host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=category,
subcategory=subcategory,
query_id=query_id,
resource=resource,
options=options)
return response
def _get(self, resource, query_id=None, options=None):
"""Queries the REST service and returns the result"""
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=self._category,
subcategory=self._subcategory,
query_id=query_id,
resource=resource,
options=options)
return response
def get(self, category, subcategory, resource, query_id=None, **options):
"""Creates the URL for querying the REST service"""
response = get(host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=category,
subcategory=subcategory,
query_id=query_id,
resource=resource,
options=options)
return response
def _get(self, resource, query_id=None, options=None):
"""Queries the REST service and returns the result"""
response = get(host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=self._category,
subcategory=self._subcategory,
query_id=query_id,
resource=resource,
options=options)
return response
def get_versions(self, **options):
# This particular REST endpoint follows the structure
# /{version}/meta/{species}/versions
"""Returns source version metadata, including source urls"""
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=self._configuration.species,
resource='versions',
options=options)
return response
def get_feature_type(self, **options):
"""Returns list of available regulatory feature types"""
# This particular REST endpoint follows the structure
# /{version}/{species}/regulatory/featureType
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=self._category,
subcategory=None,
resource='featureType',
options=options)
return response
def get_info(self, **options):
"""Returns general information"""
# This particular REST endpoint follows the structure
# /{version}/{species}/info
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=None,
subcategory=None,
resource='info',
options=options)
return response
def about(self, **options):
# This particular REST endpoint follows the structure
# /{version}/meta/about
"""Returns info about CellBase code"""
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=None,
resource='about',
options=options)
return response
def get_feature_type(self, **options):
"""Returns list of available regulatory feature types"""
# This particular REST endpoint follows the structure
# /{version}/{species}/regulatory/featureType
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=self._category,
subcategory=None,
resource='featureType',
options=options)
return response
def search(self, **options):
"""Returns regulatory elements"""
# This particular REST endpoint follows the structure
# /{version}/{species}/regulatory/search
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=self._category,
subcategory=None,
resource='search',
options=options)
return response
def ping(self, **options):
"""Checks if service is alive"""
# This particular REST endpoint follows the structure
# /{version}/meta/ping
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=None,
resource='ping',
options=options)
return response
def get_species(self, **options):
"""Returns available species"""
# This particular REST endpoint follows the structure
# /{version}/meta/species
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=None,
resource='species',
options=options)
return response
def get_versions(self, **options):
# This particular REST endpoint follows the structure
# /{version}/meta/{species}/versions
"""Returns source version metadata, including source urls"""
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=self._configuration.species,
resource='versions',
options=options)
return response
def about(self, **options):
# This particular REST endpoint follows the structure
# /{version}/meta/about
"""Returns info about CellBase code"""
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=None,
resource='about',
options=options)
return response
def ping(self, **options):
"""Checks if service is alive"""
# This particular REST endpoint follows the structure
# /{version}/meta/ping
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=None,
resource='ping',
options=options)
return response
def get_info(self, **options):
"""Returns general information"""
# This particular REST endpoint follows the structure
# /{version}/{species}/info
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=None,
subcategory=None,
resource='info',
options=options)
return response
def search(self, **options):
"""Returns regulatory elements"""
# This particular REST endpoint follows the structure
# /{version}/{species}/regulatory/search
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=self._configuration.species,
category=self._category,
subcategory=None,
resource='search',
options=options)
return response
def test_get_multiple_ids(self):
"""Tests the retrieval of information for multiple IDs"""
# Normal query with string ids
res = get(session=self._session,
host=self._host,
version=self._version,
species=self._species,
category='feature',
subcategory='gene',
resource='snp',
query_id='BRCA1,BRCA2,LDLR')
self.check_counts(res)
def get_species(self, **options):
"""Returns available species"""
# This particular REST endpoint follows the structure
# /{version}/meta/species
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=None,
resource='species',
options=options)
return response
def get_help(self, method_name=None, show_params=False, **options):
# Getting swagger documentation
response = get(session=self._session,
host=self._configuration.host,
version='swagger.json',
species=None,
category=None,
subcategory=None,
resource=None,
options=options)
sys.stdout.write(self.__class__.__name__ + '\n')
# Getting class methods
methods = [
func for func in dir(self)
if callable(getattr(self, func)) and not func.startswith('_')
]
text = '{indent}{bullet} {name}: {desc}\n'
for method in methods:
if method_name is not None and method_name != method:
continue
# Getting method info
method_swag = (method[4:] if method.startswith('get_') else method)
path_info = [response['paths'][path] for path in response['paths']
if self._category in path and method_swag in path]
if not path_info:
continue
desc = path_info[0]['get']['summary']
desc = desc.replace('http://bioinfo.hpc.cam.ac.uk/cellbase',
self._configuration.host)
sys.stdout.write(text.format(indent=' ' * 4,
bullet='-',
name=method,
desc=desc))
# Getting method parameters
if not show_params:
continue
for param in path_info[0]['get']['parameters']:
if param['name'] in ['version', 'species', 'Output format']:
continue
desc = param['description']
desc = desc.replace('http://bioinfo.hpc.cam.ac.uk/cellbase',
self._configuration.host)
sys.stdout.write(text.format(indent=' ' * 8,
bullet='*',
name=param['name'],
desc=desc))
def test_duplicated_ids(self):
"""Tests the retrieval of information for duplicated IDs"""
# Modifying the number of ids needed for multithreading
get.__globals__['_CALL_BATCH_SIZE'] = 5
# Normal query
n = 10 # Number of duplications
res = get(host=self._host, version=self._version,
species=self._species, category='feature', subcategory='gene',
resource='snp', query_id=','.join(['LDLR']*n))
assert len(res) == n
# Checking that every response has the same number of results
for i, r in enumerate(res):
assert len(r['result']) == 4108
def test_multiple_threads_with_skip(self):
"""Tests the retrieval of information with multiple threads with skip"""
res = get(session=self._session,
host=self._host,
version=self._version,
species=self._species,
category='feature',
subcategory='gene',
resource='snp',
query_id='BRCA1,BRCA2,LDLR',
options={'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4152
assert len(res[1]['result']) == 6419
assert len(res[2]['result']) == 108
def test_get_multiple_ids_with_list_ids(self):
"""Query with skip"""
res = get(session=self._session,
host=self._host,
version=self._version,
species=self._species,
category='feature',
subcategory='gene',
resource='snp',
query_id='BRCA1,BRCA2,LDLR',
options={'skip': 4000})
assert len(res) == 3
assert len(res[0]['result']) == 4152
assert len(res[1]['result']) == 6419
assert len(res[2]['result']) == 108
def test_multiple_threads(self):
"""Tests the retrieval of information with multiple threads"""
# Modifying the number of ids needed for multithreading
get.__globals__['_CALL_BATCH_SIZE'] = 2
# Normal query
res = get(session=self._session,
host=self._host,
version=self._version,
species=self._species,
category='feature',
subcategory='gene',
resource='snp',
query_id='BRCA1,BRCA2,LDLR')
self.check_counts(res)
def test_multiple_threads_with_limit(self):
"""Tests the retrieval of information with multiple threads with limit"""
# Query with limit
res = get(session=self._session,
host=self._host,
version=self._version,
species=self._species,
category='feature',
subcategory='gene',
resource='snp',
query_id='BRCA1,BRCA2,LDLR',
options={'limit': 8000})
assert len(res) == 3
assert len(res[0]['result']) == 8000
assert len(res[1]['result']) == 8000
assert len(res[2]['result']) == 4108
def get_category(self, query_id, **options):
# This particular REST endpoint follows the structure
# /{version}/meta/{category}
"""Returns source version metadata, including source urls"""
categories = ['feature', 'genomic', 'network', 'regulatory']
if query_id not in categories:
msg = 'Query has to be one of the following: ' + str(categories)
raise ValueError(msg)
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=None,
resource=query_id,
options=options)
return response
def get_category(self, query_id, **options):
# This particular REST endpoint follows the structure
# /{version}/meta/{category}
"""Returns source version metadata, including source urls"""
categories = ['feature', 'genomic', 'network', 'regulatory']
if query_id not in categories:
msg = 'Query has to be one of the following: ' + str(categories)
raise ValueError(msg)
response = get(session=self._session,
host=self._configuration.host,
version=self._configuration.version,
species=None,
category=self._category,
subcategory=None,
resource=query_id,
options=options)
return response
