def __init__(self, config_client=None):
# Initializing session
self._session = requests.Session()
self._session.headers.update({"Accept-Encoding": "gzip"})
# CellBase REST clients
self._gene_client = None
self._transcript_client = None
self._protein_client = None
self._variation_client = None
self._xref_client = None
self._region_client = None
self._variant_client = None
self._genome_sequence_client = None
self._clinical_client = None
self._tfbs_client = None
self._regulation_client = None
self._species_client = None
self._meta_client = None
# Setting up config params
if config_client is not None:
if isinstance(config_client, ConfigClient):
self._configuration = config_client
else:
msg = ('CellBaseClient configuration not properly set.' +
' "pycellbase.config.ConfigClient" object is needed as' +
' parameter')
raise ValueError(msg)
else:
self._configuration = ConfigClient()
def test_get_default_config(self):
# Initialization
cc = ConfigClient()
cbc = CellBaseClient(cc)
assert cc.get_default_configuration() == cbc.get_default_configuration(
)
def test_init_config_dict(self):
"""Checks retrieval of configuration params from config files"""
# Default parameters
cc = ConfigClient()
assert cc.species == 'hsapiens'
assert cc.version == 'v4'
# Retrieving config params from config dict
cc = ConfigClient({'species': 'mmusculus'})
assert cc.species == 'mmusculus'
assert cc.version == 'v4'
cc = ConfigClient({'species': 'mmusculus', 'version': 'v3'})
assert cc.species == 'mmusculus'
assert cc.version == 'v3'
def test_change_config(self):
"""Checks configuration customization"""
# Initialization
cc = ConfigClient()
cbc = CellBaseClient(cc)
# Checking some default config params
assert cbc.get_config()['species'] == 'hsapiens'
assert cbc.get_config()['version'] == 'v4'
# Checking some setters for config params
cc.species = 'mmusculus'
assert cbc.get_config()['species'] == 'mmusculus'
cc.version = 'v3'
assert cbc.get_config()['version'] == 'v3'
def test_change_config(self):
"""Checks configuration customization"""
# Initialization
cc = ConfigClient()
cbc = CellBaseClient(cc)
# Checking some default config params
assert cbc.get_config()['species'] == 'hsapiens'
assert cbc.get_config()['version'] == 'latest'
# Checking some setters for config params
cc.species = 'mmusculus'
assert cbc.get_config()['species'] == 'mmusculus'
cc.version = 'v4'
assert cbc.get_config()['version'] == 'v4'
def test_init_config(self):
"""Checks retrieval of configuration params from config files"""
# Default parameters
cc = ConfigClient()
assert cc.species == 'hsapiens'
assert cc.version == 'latest'
# Retrieving config params from YAML config file
cc = ConfigClient('../resources/config.yml')
assert cc.species == 'mmusculus'
assert cc.version == 'v4'
# Retrieving config params from JSON config file
cc = ConfigClient('../resources/config.json')
assert cc.species == 'celegans'
assert cc.version == 'latest'
def setUp(self):
"""Initializes config params"""
cc = ConfigClient()
self._host = cc.host
self._version = cc.version
self._species = cc.species
self._session = Session()
def test_get(self):
""""Checks generic fetcher for RESTful service"""
# Initialization
cc = ConfigClient()
cbc = CellBaseClient(cc)
res = cbc.get('feature', 'gene', 'protein', 'BRCA1')
assert res[0]['result'][0]['name'][0] == 'BRCA1_HUMAN'
def __init__(self, config_client=None):
# Client storage; If a client is already created, then it is returned
self._clients = {}
# Setting up config params
if config_client is not None:
try:
assert isinstance(config_client, ConfigClient)
except:
msg = (
'CellBaseClient configuration not properly set.' +
' "pycellbase.config.ConfigClient" object is needed as' +
' parameter')
raise IOError(msg)
self._configuration = config_client
else:
self._configuration = ConfigClient()
def setUp(self):
"""Initializes the variation client"""
self._vc = cbfts.VariationClient(ConfigClient())
class CellBaseClient(object):
"""Creates different query clients and allows direct queries to the RESTful
service"""
def __init__(self, config_client=None):
# Initializing session
self._session = requests.Session()
self._session.headers.update({"Accept-Encoding": "gzip"})
# CellBase REST clients
self._gene_client = None
self._transcript_client = None
self._protein_client = None
self._variation_client = None
self._xref_client = None
self._region_client = None
self._variant_client = None
self._genome_sequence_client = None
self._clinical_client = None
self._tfbs_client = None
self._regulation_client = None
self._species_client = None
self._meta_client = None
# Setting up config params
if config_client is not None:
if isinstance(config_client, ConfigClient):
self._configuration = config_client
else:
msg = ('CellBaseClient configuration not properly set.' +
' "pycellbase.config.ConfigClient" object is needed as' +
' parameter')
raise ValueError(msg)
else:
self._configuration = ConfigClient()
def show_configuration(self):
"""Returns current configuration parameters"""
return self._configuration.configuration
def get_default_configuration(self):
return self._configuration.get_default_configuration()
def get(self, category, subcategory, resource, query_id=None, **options):
"""Creates the URL for querying the REST service"""
response = get(session=self._session,
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_gene_client(self):
"""Creates the gene client"""
if self._gene_client is None:
self._gene_client = crc.GeneClient(self._session,
self._configuration)
return self._gene_client
def get_transcript_client(self):
"""Creates the protein client"""
if self._transcript_client is None:
self._transcript_client = crc.TranscriptClient(self._session,
self._configuration)
return self._transcript_client
def get_protein_client(self):
"""Creates the protein client"""
if self._protein_client is None:
self._protein_client = crc.ProteinClient(self._session,
self._configuration)
return self._protein_client
def get_variation_client(self):
"""Creates the variation client"""
if self._variation_client is None:
self._variation_client = crc.VariationClient(self._session,
self._configuration)
return self._variation_client
def get_xref_client(self):
"""Creates the xref client"""
if self._xref_client is None:
self._xref_client = crc.XrefClient(self._session,
self._configuration)
return self._xref_client
def get_region_client(self):
"""Creates the region client"""
if self._region_client is None:
self._region_client = crc.RegionClient(self._session,
self._configuration)
return self._region_client
@deprecated
def get_genomic_region_client(self):
return self.get_region_client()
def get_variant_client(self):
"""Creates the variant client"""
if self._variant_client is None:
self._variant_client = crc.VariantClient(self._session,
self._configuration)
return self._variant_client
def get_genome_sequence_client(self):
"""Creates the genome sequence client"""
if self._genome_sequence_client is None:
self._genome_sequence_client = \
crc.GenomeSequenceClient(self._session,
self._configuration)
return self._genome_sequence_client
def get_clinical_client(self):
"""Creates the clinical client"""
if self._clinical_client is None:
self._clinical_client = crc.ClinicalClient(self._session,
self._configuration)
return self._clinical_client
def get_tfbs_client(self):
"""Creates the TFBS client"""
if self._tfbs_client is None:
self._tfbs_client = crc.TFBSClient(self._session,
self._configuration)
return self._tfbs_client
def get_regulation_client(self):
"""Creates the regulatory client"""
if self._regulation_client is None:
self._regulation_client = crc.RegulationClient(self._session,
self._configuration)
return self._regulation_client
def get_species_client(self):
"""Creates the regulatory client"""
if self._species_client is None:
self._species_client = crc.SpeciesClient(self._session,
self._configuration)
return self._species_client
def get_meta_client(self):
"""Creates the clinical client"""
if self._meta_client is None:
self._meta_client = crc.MetaClient(self._session,
self._configuration)
return self._meta_client
def setUp(self):
"""Initializes the variation client"""
self._gr = cbfts.RegionClient(Session(), ConfigClient())
def setUp(self):
"""Initializes the variation client"""
self._gr = cbfts.GenomicRegionClient(ConfigClient())
def setUp(self):
"""Initializes the transcript client"""
self._tc = cbfts.TranscriptClient(Session(), ConfigClient())
def setUp(self):
"""Initializes the gene client"""
self._gc = cbfts.GeneClient(Session(), ConfigClient())
def setUp(self):
"""Initializes the protein client"""
self._pc = cbfts.ProteinClient(Session(), ConfigClient())
def setUp(self):
"""Initializes the variation client"""
self._vc = cbfts.VariantClient(Session(), ConfigClient())