def get_provenance(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
result = taxon_api.get_provenance()
self.logger.info(result)
return [ttypes.ObjectProvenanceAction(**x) for x in result]
def setup():
shared.setup()
global t_new, t_new_e, t_old, t_old_e
t_new = TaxonAPI(shared.services, shared.token, taxon_new)
t_new_e = _Prototype(shared.services, shared.token, taxon_new)
t_old = TaxonAPI(shared.services, shared.token, taxon_old)
t_old_e = _KBaseGenomes_Genome(shared.services, shared.token, taxon_old)
def get_history(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
result = taxon_api.get_history()
self.logger.info(result)
return [ttypes.ObjectInfo(**x) for x in result]
def setup():
shared.setup()
global t_new, t_new_e, t_old, t_old_e, t_client_new, t_client_old
t_new = TaxonAPI(shared.services, shared.token, taxon_new)
t_new_e = _Taxon(shared.services, shared.token, taxon_new)
t_old = TaxonAPI(shared.services, shared.token, taxon_old)
t_old_e = _KBaseGenomes_Genome(shared.services, shared.token, taxon_old)
_log.info("Connecting to Taxon Thrift Service at {}".format(shared.services["taxon_service_url"]))
t_client_new = TaxonClientAPI(shared.services["taxon_service_url"], shared.token, taxon_new)
t_client_old = TaxonClientAPI(shared.services["taxon_service_url"], shared.token, taxon_old)
def fetch_and_print_taxon(ws_url='https://ci.kbase.us/services/ws/'):
"""Fetch Taxon from Workspace Service.
Args:
ws_url (str): a service address or a local directory
containing a downloaded version of the data created with the
``dump_wsfile`` utility.
"""
# Initialize API with target object
taxon_ref = 'ReferenceTaxons/242159_taxon'
# Try to connect to remote service
taxon = TaxonAPI(token=os.environ.get('KB_AUTH_TOKEN'), ref=taxon_ref,
services={'workspace_service_url': ws_url})
# Now the methods of the instance can be used to fetch and show
# taxonomic information
print('Got taxon "{} ({})"'.format(taxon.get_scientific_name(),
taxon.get_taxonomic_id()))
def fetch_and_print_taxon(ws_url='https://ci.kbase.us/services/ws/'):
"""Fetch Taxon from Workspace Service.
Args:
ws_url (str): a service address or a local directory
containing a downloaded version of the data created with the
``dump_wsfile`` utility.
"""
# Initialize API with target object
taxon_ref = 'ReferenceTaxons/242159_taxon'
# Try to connect to remote service
taxon = TaxonAPI(token=os.environ.get('KB_AUTH_TOKEN'),
ref=taxon_ref,
services={'workspace_service_url': ws_url})
# Now the methods of the instance can be used to fetch and show
# taxonomic information
print('Got taxon "{} ({})"'.format(taxon.get_scientific_name(),
taxon.get_taxonomic_id()))
def test_bogus_type():
inputs = ["Bogus",
"ReferenceGenomeAnnotations/kb|g.166819",
"ReferenceGenomeAnnotations/kb|g.166819_assembly",
"OriginalReferenceGenomes/kb|g.166819.contigset"]
_log.info("Input {}".format(inputs))
for x in inputs:
try:
t = TaxonAPI(shared.services, shared.token, x)
except Exception, e:
assert isinstance(e, TypeError)
def get_info(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
result = taxon_api.get_info()
return ttypes.ObjectInfo(**result)
def get_genetic_code(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_genetic_code()
def get_aliases(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_aliases()
def get_domain(self, token=None, ref=None):
try:
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_domain()
except Exception, e:
raise ttypes.ServiceException(e.message, traceback.print_exc(), "get_domain", {"ref": str(ref)})
def get_taxonomic_id(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_taxonomic_id()
def get_scientific_name(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_scientific_name()
def get_genome_annotations(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_genome_annotations(ref_only=True)
def get_children(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_children(ref_only=True)
def get_domain(self, token=None, ref=None):
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_domain()
def get_genome_annotations(self, token=None, ref=None):
try:
taxon_api = TaxonAPI(self.services, token, ref)
return taxon_api.get_genome_annotations(ref_only=True)
except Exception, e:
raise ttypes.ServiceException(e.message, traceback.print_exc(), "get_genome_annotation", {"ref": str(ref)})
