def test_api_service(service_name='assembly',apiurl='http://localhost',token=None):
try:
if service_name == "taxon":
#from doekbase.data_api.taxonomy.taxon.service import thrift_client
from doekbase.data_api.taxonomy.taxon.api import TaxonClientAPI
api = TaxonClientAPI(apiurl, token, 'ReferenceTaxons/242159_taxon')
elif service_name == "assembly":
#from doekbase.data_api.sequence.assembly.service import thrift_client
from doekbase.data_api.sequence.assembly.api import AssemblyClientAPI
api = AssemblyClientAPI(apiurl, token, 'ReferenceGenomeAnnotations/kb|g.166819_assembly')
elif service_name == "genome_annotation":
#from doekbase.data_api.annotation.genome_annotation.service import thrift_client
from doekbase.data_api.annotation.genome_annotation.api import GenomeAnnotationClientAPI
api = GenomeAnnotationClientAPI(apiurl, token, 'ReferenceGenomeAnnotations/kb|g.166819')
else:
raise Exception("Service not activated: {}".format(service_name))
except Exception as e:
print '3 ' + service_name + '_api - UNKNOWN - could not load client library for ' + service_name + ' ' + str(sys.path) + ' ' + str(sys.exc_info()[0])
raise
if service_name == 'genome_annotation':
try:
feature_types = api.get_feature_types()
if 'CDS' in feature_types:
print '0 ' + service_name + '_api - OK - feature_type returned ' + str(feature_types)
else:
print '2 ' + service_name + '_api - CRITICAL - unexpected feature_types returned ' + str(feature_types)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(sys.exc_info()[0])
if service_name == 'taxon':
try:
lineage = api.get_scientific_lineage()
if 'Ostreococcus' in lineage:
print '0 ' + service_name + '_api - OK - expected lineage OK ' + str(lineage)
else:
print '2 ' + service_name + '_api - CRITICAL - unexpected lineage ' + str(lineage)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(sys.exc_info()[0])
if service_name == 'assembly':
try:
stats = api.get_stats()
ref_num_contigs=21
if stats['num_contigs']==ref_num_contigs:
print '0 ' + service_name + '_api - OK - ' + str(ref_num_contigs) + ' contigs found'
else:
print '2 ' + service_name + '_api - CRITICAL - ' + str(stats['num_contigs']) + ' contigs found, not ' + str(ref_num_contigs)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(sys.exc_info()[0])
def test_api_service(service_name='assembly',
apiurl='http://localhost',
token=None):
try:
if service_name == "taxon":
#from doekbase.data_api.taxonomy.taxon.service import thrift_client
from doekbase.data_api.taxonomy.taxon.api import TaxonClientAPI
api = TaxonClientAPI(apiurl, token, 'ReferenceTaxons/242159_taxon')
elif service_name == "assembly":
#from doekbase.data_api.sequence.assembly.service import thrift_client
from doekbase.data_api.sequence.assembly.api import AssemblyClientAPI
api = AssemblyClientAPI(
apiurl, token,
'ReferenceGenomeAnnotations/kb|g.166819_assembly')
elif service_name == "genome_annotation":
#from doekbase.data_api.annotation.genome_annotation.service import thrift_client
from doekbase.data_api.annotation.genome_annotation.api import GenomeAnnotationClientAPI
api = GenomeAnnotationClientAPI(
apiurl, token, 'ReferenceGenomeAnnotations/kb|g.166819')
else:
raise Exception("Service not activated: {}".format(service_name))
except Exception as e:
print '3 ' + service_name + '_api - UNKNOWN - could not load client library for ' + service_name + ' ' + str(
sys.path) + ' ' + str(sys.exc_info()[0])
raise
if service_name == 'genome_annotation':
try:
feature_types = api.get_feature_types()
if 'CDS' in feature_types:
print '0 ' + service_name + '_api - OK - feature_type returned ' + str(
feature_types)
else:
print '2 ' + service_name + '_api - CRITICAL - unexpected feature_types returned ' + str(
feature_types)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(
sys.exc_info()[0])
if service_name == 'taxon':
try:
lineage = api.get_scientific_lineage()
if 'Ostreococcus' in lineage:
print '0 ' + service_name + '_api - OK - expected lineage OK ' + str(
lineage)
else:
print '2 ' + service_name + '_api - CRITICAL - unexpected lineage ' + str(
lineage)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(
sys.exc_info()[0])
if service_name == 'assembly':
try:
stats = api.get_stats()
ref_num_contigs = 21
if stats['num_contigs'] == ref_num_contigs:
print '0 ' + service_name + '_api - OK - ' + str(
ref_num_contigs) + ' contigs found'
else:
print '2 ' + service_name + '_api - CRITICAL - ' + str(
stats['num_contigs']) + ' contigs found, not ' + str(
ref_num_contigs)
except:
print '2 ' + service_name + '_api - CRITICAL - unexpected error encountered ' + str(
sys.exc_info()[0])
