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 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_client(): ap = argparse.ArgumentParser() ap.add_argument('--ref', default='ReferenceTaxons/242159_taxon', help='Object reference ID, e.g. 1019/4/1') ap.add_argument('--url', dest='url', default='http://localhost:9101', metavar='URL', help='Remote server url ' '(default=%(default)s)') args = ap.parse_args() token = '' if os.environ.has_key('KB_AUTH_TOKEN'): token = os.environ['KB_AUTH_TOKEN'] api = TaxonClientAPI(args.url, token, args.ref) print("Getting data..") t0 = time.time() object_info = api.get_info() dt = time.time() - t0 print object_info print("Got and parsed data from get_info in {:g} seconds".format(dt)) t0 = time.time() history = api.get_history() dt = time.time() - t0 print history print("Got and parsed data from get_history in {:g} seconds".format(dt)) t0 = time.time() provenance = api.get_provenance() dt = time.time() - t0 print provenance print("Got and parsed data from get_provenance in {:g} seconds".format(dt)) t0 = time.time() id = api.get_id() dt = time.time() - t0 print id print("Got and parsed data from get_id in {:g} seconds".format(dt)) t0 = time.time() name = api.get_name() dt = time.time() - t0 print name print("Got and parsed data from get_name in {:g} seconds".format(dt)) t0 = time.time() version = api.get_version() dt = time.time() - t0 print version print("Got and parsed data from get_version in {:g} seconds".format(dt)) t0 = time.time() genetic_code = api.get_genetic_code() dt = time.time() - t0 print genetic_code print( "Got and parsed data from get_genetic_code in {:g} seconds".format(dt)) t0 = time.time() aliases = api.get_aliases() dt = time.time() - t0 print aliases print("Got and parsed data from get_aliases in {:g} seconds".format(dt)) t0 = time.time() domain = api.get_domain() dt = time.time() - t0 print domain print("Got and parsed data from get_domain in {:g} seconds".format(dt)) try: t0 = time.time() kingdom = api.get_kingdom() dt = time.time() - t0 print kingdom print( "Got and parsed data from get_kingdom in {:g} seconds".format(dt)) except: pass t0 = time.time() taxonomic_id = api.get_taxonomic_id() dt = time.time() - t0 print taxonomic_id print( "Got and parsed data from get_taxonomic_id in {:g} seconds".format(dt)) t0 = time.time() scientific_lineage = api.get_scientific_lineage() dt = time.time() - t0 print scientific_lineage print("Got and parsed data from get_scientific_lineage in {:g} seconds". format(dt)) t0 = time.time() genome_annotations = api.get_genome_annotations() dt = time.time() - t0 print genome_annotations print("Got and parsed data from get_genome_annotations in {:g} seconds". format(dt)) t0 = time.time() parent = api.get_parent() dt = time.time() - t0 print parent print("Got and parsed data from get_parent in {:g} seconds".format(dt)) t0 = time.time() children = api.get_children() dt = time.time() - t0 print children print("Got and parsed data from get_children in {:g} seconds".format(dt))
def test_client(): ap = argparse.ArgumentParser() ap.add_argument('--ref', default='ReferenceTaxons/242159_taxon', help='Object reference ID, e.g. 1019/4/1') ap.add_argument('--url', dest='url', default='http://localhost:9101', metavar='URL', help='Remote server url ' '(default=%(default)s)') args = ap.parse_args() token=''; if os.environ.has_key('KB_AUTH_TOKEN'): token = os.environ['KB_AUTH_TOKEN'] api = TaxonClientAPI(args.url, token, args.ref) print("Getting data..") t0 = time.time() object_info = api.get_info() dt = time.time() - t0 print object_info print("Got and parsed data from get_info in {:g} seconds".format(dt)) t0 = time.time() history = api.get_history() dt = time.time() - t0 print history print("Got and parsed data from get_history in {:g} seconds".format(dt)) t0 = time.time() provenance = api.get_provenance() dt = time.time() - t0 print provenance print("Got and parsed data from get_provenance in {:g} seconds".format(dt)) t0 = time.time() id = api.get_id() dt = time.time() - t0 print id print("Got and parsed data from get_id in {:g} seconds".format(dt)) t0 = time.time() name = api.get_name() dt = time.time() - t0 print name print("Got and parsed data from get_name in {:g} seconds".format(dt)) t0 = time.time() version = api.get_version() dt = time.time() - t0 print version print("Got and parsed data from get_version in {:g} seconds".format(dt)) t0 = time.time() genetic_code = api.get_genetic_code() dt = time.time() - t0 print genetic_code print("Got and parsed data from get_genetic_code in {:g} seconds".format(dt)) t0 = time.time() aliases = api.get_aliases() dt = time.time() - t0 print aliases print("Got and parsed data from get_aliases in {:g} seconds".format(dt)) t0 = time.time() domain = api.get_domain() dt = time.time() - t0 print domain print("Got and parsed data from get_domain in {:g} seconds".format(dt)) try: t0 = time.time() kingdom = api.get_kingdom() dt = time.time() - t0 print kingdom print("Got and parsed data from get_kingdom in {:g} seconds".format(dt)) except: pass t0 = time.time() taxonomic_id = api.get_taxonomic_id() dt = time.time() - t0 print taxonomic_id print("Got and parsed data from get_taxonomic_id in {:g} seconds".format(dt)) t0 = time.time() scientific_lineage = api.get_scientific_lineage() dt = time.time() - t0 print scientific_lineage print("Got and parsed data from get_scientific_lineage in {:g} seconds".format(dt)) t0 = time.time() genome_annotations = api.get_genome_annotations() dt = time.time() - t0 print genome_annotations print("Got and parsed data from get_genome_annotations in {:g} seconds".format(dt)) t0 = time.time() parent = api.get_parent() dt = time.time() - t0 print parent print("Got and parsed data from get_parent in {:g} seconds".format(dt)) t0 = time.time() children = api.get_children() dt = time.time() - t0 print children print("Got and parsed data from get_children in {:g} seconds".format(dt))
def test_client(): ap = argparse.ArgumentParser() ap.add_argument('--ref', default='ReferenceTaxons/83333_taxon', help='Object reference ID, e.g. 1019/4/1') ap.add_argument('--host', dest='host', default='localhost', metavar='ADDR', help='Remote server host ' '(default=%(default)s)') ap.add_argument('--port', dest='port', default=9090, metavar='PORT', help='Remote server port ' '(default=%(default)d)') args = ap.parse_args() api = TaxonClientAPI(args.host, args.port, os.environ["KB_AUTH_TOKEN"], args.ref) print("Getting data..") t0 = time.time() genetic_code = api.get_genetic_code() dt = time.time() - t0 print genetic_code print("Got and parsed data in {:g} seconds".format(dt)) t0 = time.time() aliases = api.get_aliases() dt = time.time() - t0 print aliases print("Got and parsed data in {:g} seconds".format(dt)) t0 = time.time() domain = api.get_domain() dt = time.time() - t0 print domain print("Got and parsed data in {:g} seconds".format(dt)) try: t0 = time.time() kingdom = api.get_kingdom() dt = time.time() - t0 print kingdom print("Got and parsed data in {:g} seconds".format(dt)) except: pass t0 = time.time() taxonomic_id = api.get_taxonomic_id() dt = time.time() - t0 print taxonomic_id print("Got and parsed data in {:g} seconds".format(dt)) t0 = time.time() scientific_lineage = api.get_scientific_lineage() dt = time.time() - t0 print scientific_lineage print("Got and parsed data in {:g} seconds".format(dt)) t0 = time.time() genome_annotations = api.get_genome_annotations() dt = time.time() - t0 print genome_annotations print("Got and parsed data in {:g} seconds".format(dt)) t0 = time.time() parent = api.get_parent() dt = time.time() - t0 print parent print("Got and parsed data in {:g} seconds".format(dt)) t0 = time.time() children = api.get_children() dt = time.time() - t0 print children print("Got and parsed data in {:g} seconds".format(dt))
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])