def __init__(self):
submod = get_service_name() or 'GenomeAnnotationFileUtil'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_GenomeAnnotationFileUtil.genbank_to_genome_annotation,
name='GenomeAnnotationFileUtil.genbank_to_genome_annotation',
types=[dict])
self.method_authentication['GenomeAnnotationFileUtil.genbank_to_genome_annotation'] = 'required'
self.rpc_service.add(impl_GenomeAnnotationFileUtil.genome_annotation_to_genbank,
name='GenomeAnnotationFileUtil.genome_annotation_to_genbank',
types=[dict])
self.method_authentication['GenomeAnnotationFileUtil.genome_annotation_to_genbank'] = 'required'
self.rpc_service.add(impl_GenomeAnnotationFileUtil.export_genome_annotation_as_genbank,
name='GenomeAnnotationFileUtil.export_genome_annotation_as_genbank',
types=[dict])
self.method_authentication['GenomeAnnotationFileUtil.export_genome_annotation_as_genbank'] = 'required'
self.rpc_service.add(impl_GenomeAnnotationFileUtil.status,
name='GenomeAnnotationFileUtil.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'IdMap'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.rpc_service.add(impl_IdMap.lookup_genome,
name='IdMap.lookup_genome',
types=[basestring, basestring])
self.rpc_service.add(impl_IdMap.lookup_features,
name='IdMap.lookup_features',
types=[basestring, list, basestring, basestring])
self.rpc_service.add(impl_IdMap.lookup_feature_synonyms,
name='IdMap.lookup_feature_synonyms',
types=[basestring, basestring])
self.rpc_service.add(impl_IdMap.longest_cds_from_locus,
name='IdMap.longest_cds_from_locus',
types=[list])
self.rpc_service.add(impl_IdMap.longest_cds_from_mrna,
name='IdMap.longest_cds_from_mrna',
types=[list])
def __init__(self):
submod = get_service_name() or 'Loader'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_Loader.import_data,
name='Loader.import_data',
types=[dict])
self.method_authentication['Loader.import_data'] = 'required'
self.rpc_service.add(impl_Loader.validate,
name='Loader.validate',
types=[dict])
self.method_authentication['Loader.validate'] = 'required'
self.rpc_service.add(impl_Loader.uploader,
name='Loader.uploader',
types=[dict])
self.method_authentication['Loader.uploader'] = 'required'
self.rpc_service.add(impl_Loader.download,
name='Loader.download',
types=[dict])
self.method_authentication['Loader.download'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'ReadsUtils'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_ReadsUtils.validateFASTQ,
name='ReadsUtils.validateFASTQ',
types=[list])
self.method_authentication['ReadsUtils.validateFASTQ'] = 'required' # noqa
self.rpc_service.add(impl_ReadsUtils.upload_reads,
name='ReadsUtils.upload_reads',
types=[dict])
self.method_authentication['ReadsUtils.upload_reads'] = 'required' # noqa
self.rpc_service.add(impl_ReadsUtils.download_reads,
name='ReadsUtils.download_reads',
types=[dict])
self.method_authentication['ReadsUtils.download_reads'] = 'required' # noqa
self.rpc_service.add(impl_ReadsUtils.export_reads,
name='ReadsUtils.export_reads',
types=[dict])
self.method_authentication['ReadsUtils.export_reads'] = 'required' # noqa
self.rpc_service.add(impl_ReadsUtils.status,
name='ReadsUtils.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'ClusterServicePy'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.rpc_service.add(impl_ClusterServicePy.estimate_k,
name='ClusterServicePy.estimate_k',
types=[dict, int, int, int, int, int])
self.rpc_service.add(impl_ClusterServicePy.estimate_k_new,
name='ClusterServicePy.estimate_k_new',
types=[dict, int, int, basestring, int, float, int, int])
self.rpc_service.add(impl_ClusterServicePy.cluster_k_means,
name='ClusterServicePy.cluster_k_means',
types=[dict, int, int, int, int, basestring])
self.rpc_service.add(impl_ClusterServicePy.cluster_hierarchical,
name='ClusterServicePy.cluster_hierarchical',
types=[dict, basestring, basestring, float, int])
self.rpc_service.add(impl_ClusterServicePy.clusters_from_dendrogram,
name='ClusterServicePy.clusters_from_dendrogram',
types=[dict, basestring, float])
self.rpc_service.add(impl_ClusterServicePy.calc_cluster_qualities,
name='ClusterServicePy.calc_cluster_qualities',
types=[list])
def __init__(self):
submod = get_service_name() or 'feature_sequence'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_feature_sequence.featureset_protein_sequence,
name='feature_sequence.featureset_protein_sequence',
types=[basestring, basestring])
self.method_authentication['feature_sequence.featureset_protein_sequence'] = 'required'
self.rpc_service.add(impl_feature_sequence.featureset_nucleotide_sequence,
name='feature_sequence.featureset_nucleotide_sequence',
types=[basestring, basestring])
self.method_authentication['feature_sequence.featureset_nucleotide_sequence'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or "ranjansample"
self.userlog = log.log(
submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file(),
)
self.serverlog = log.log(
submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file(),
)
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_ranjansample.myfunc1, name="ranjansample.myfunc1", types=[basestring, basestring])
self.method_authentication["ranjansample.myfunc1"] = "required"
self.auth_client = biokbase.nexus.Client(
config={"server": "nexus.api.globusonline.org", "verify_ssl": True, "client": None, "client_secret": None}
)
def __init__(self):
submod = get_service_name() or 'CoExpression'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_CoExpression.filter_genes,
name='CoExpression.filter_genes',
types=[dict])
self.method_authentication['CoExpression.filter_genes'] = 'required'
self.rpc_service.add(impl_CoExpression.const_coex_net_clust,
name='CoExpression.const_coex_net_clust',
types=[dict])
self.method_authentication['CoExpression.const_coex_net_clust'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': False,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'IDServerAPI'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.rpc_service.add(impl_IDServerAPI.kbase_ids_to_external_ids,
name='IDServerAPI.kbase_ids_to_external_ids',
types=[list])
self.rpc_service.add(impl_IDServerAPI.external_ids_to_kbase_ids,
name='IDServerAPI.external_ids_to_kbase_ids',
types=[basestring, list])
self.rpc_service.add(impl_IDServerAPI.register_ids,
name='IDServerAPI.register_ids',
types=[basestring, basestring, list])
self.rpc_service.add(impl_IDServerAPI.allocate_id_range,
name='IDServerAPI.allocate_id_range',
types=[basestring, int])
self.rpc_service.add(impl_IDServerAPI.register_allocated_ids,
name='IDServerAPI.register_allocated_ids',
types=[basestring, basestring, dict])
self.rpc_service.add(impl_IDServerAPI.get_identifier_prefix,
name='IDServerAPI.get_identifier_prefix',
types=[])
def __init__(self):
submod = get_service_name() or 'KBaseGenomeUtil'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_KBaseGenomeUtil.index_genomes,
name='KBaseGenomeUtil.index_genomes',
types=[dict])
self.method_authentication['KBaseGenomeUtil.index_genomes'] = 'required'
self.rpc_service.add(impl_KBaseGenomeUtil.blast_against_genome,
name='KBaseGenomeUtil.blast_against_genome',
types=[dict])
self.method_authentication['KBaseGenomeUtil.blast_against_genome'] = 'required'
self.rpc_service.add(impl_KBaseGenomeUtil.filter_BlastOutput,
name='KBaseGenomeUtil.filter_BlastOutput',
types=[dict])
self.method_authentication['KBaseGenomeUtil.filter_BlastOutput'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'mikaelacashmancontigfilterkbase'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_mikaelacashmancontigfilterkbase.filter_contigs,
name='mikaelacashmancontigfilterkbase.filter_contigs',
types=[dict])
self.method_authentication['mikaelacashmancontigfilterkbase.filter_contigs'] = 'required'
self.rpc_service.add(impl_mikaelacashmancontigfilterkbase.filter_contigs_max,
name='mikaelacashmancontigfilterkbase.filter_contigs_max',
types=[dict])
self.method_authentication['mikaelacashmancontigfilterkbase.filter_contigs_max'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'CompressionBasedDistance'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_CompressionBasedDistance.version,
name='CompressionBasedDistance.version',
types=[])
self.method_authentication['CompressionBasedDistance.version'] = 'required'
self.rpc_service.add(impl_CompressionBasedDistance.build_matrix,
name='CompressionBasedDistance.build_matrix',
types=[dict])
self.method_authentication['CompressionBasedDistance.build_matrix'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'FeatureSetUtils'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_FeatureSetUtils.upload_featureset_from_diff_expr,
name='FeatureSetUtils.upload_featureset_from_diff_expr',
types=[dict])
self.method_authentication['FeatureSetUtils.upload_featureset_from_diff_expr'] = 'required' # noqa
self.rpc_service.add(impl_FeatureSetUtils.calculate_average_expression_matrix,
name='FeatureSetUtils.calculate_average_expression_matrix',
types=[dict])
self.method_authentication['FeatureSetUtils.calculate_average_expression_matrix'] = 'required' # noqa
self.rpc_service.add(impl_FeatureSetUtils.featureset_to_tsv_file,
name='FeatureSetUtils.featureset_to_tsv_file',
types=[dict])
self.method_authentication['FeatureSetUtils.featureset_to_tsv_file'] = 'required' # noqa
self.rpc_service.add(impl_FeatureSetUtils.export_featureset_as_tsv_file,
name='FeatureSetUtils.export_featureset_as_tsv_file',
types=[dict])
self.method_authentication['FeatureSetUtils.export_featureset_as_tsv_file'] = 'required' # noqa
self.rpc_service.add(impl_FeatureSetUtils.status,
name='FeatureSetUtils.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'QIIME'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_QIIME.pick_closed_reference_otus,
name='QIIME.pick_closed_reference_otus',
types=[dict])
self.method_authentication['QIIME.pick_closed_reference_otus'] = 'required'
self.rpc_service.add(impl_QIIME.create_parameters_configuration,
name='QIIME.create_parameters_configuration',
types=[dict])
self.method_authentication['QIIME.create_parameters_configuration'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'WipeDev03'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_WipeDev03.wipe_dev03,
name='WipeDev03.wipe_dev03',
types=[])
self.method_authentication['WipeDev03.wipe_dev03'] = 'required'
self.rpc_service.add(impl_WipeDev03.shut_down_workspace,
name='WipeDev03.shut_down_workspace',
types=[])
self.method_authentication['WipeDev03.shut_down_workspace'] = 'required'
self.rpc_service.add(impl_WipeDev03.restart_workspace,
name='WipeDev03.restart_workspace',
types=[])
self.method_authentication['WipeDev03.restart_workspace'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': False,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'HandleMngr'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_HandleMngr.is_readable,
name='HandleMngr.is_readable',
types=[basestring, basestring])
self.method_authentication['HandleMngr.is_readable'] = 'optional'
self.rpc_service.add(impl_HandleMngr.add_read_acl,
name='HandleMngr.add_read_acl',
types=[list, basestring])
self.method_authentication['HandleMngr.add_read_acl'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'pavel_sdk_test_python'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_pavel_sdk_test_python.count_contigs,
name='pavel_sdk_test_python.count_contigs',
types=[basestring, basestring])
self.method_authentication['pavel_sdk_test_python.count_contigs'] = 'required'
self.rpc_service.add(impl_pavel_sdk_test_python.get_person,
name='pavel_sdk_test_python.get_person',
types=[basestring])
self.method_authentication['pavel_sdk_test_python.get_person'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'AssemblyUtil'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_AssemblyUtil.get_assembly_as_fasta,
name='AssemblyUtil.get_assembly_as_fasta',
types=[dict])
self.method_authentication['AssemblyUtil.get_assembly_as_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.export_assembly_as_fasta,
name='AssemblyUtil.export_assembly_as_fasta',
types=[dict])
self.method_authentication['AssemblyUtil.export_assembly_as_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.save_assembly_from_fasta,
name='AssemblyUtil.save_assembly_from_fasta',
types=[dict])
self.method_authentication['AssemblyUtil.save_assembly_from_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.status,
name='AssemblyUtil.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'kb_muscle'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_kb_muscle.MUSCLE_nuc,
name='kb_muscle.MUSCLE_nuc',
types=[dict])
self.method_authentication['kb_muscle.MUSCLE_nuc'] = 'required' # noqa
self.rpc_service.add(impl_kb_muscle.MUSCLE_prot,
name='kb_muscle.MUSCLE_prot',
types=[dict])
self.method_authentication['kb_muscle.MUSCLE_prot'] = 'required' # noqa
self.rpc_service.add(impl_kb_muscle.status,
name='kb_muscle.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'kb_cummerbund'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_kb_cummerbund.generate_cummerbund_plots,
name='kb_cummerbund.generate_cummerbund_plots',
types=[dict])
self.method_authentication['kb_cummerbund.generate_cummerbund_plots'] = 'required'
self.rpc_service.add(impl_kb_cummerbund.create_expression_matrix,
name='kb_cummerbund.create_expression_matrix',
types=[dict])
self.method_authentication['kb_cummerbund.create_expression_matrix'] = 'required'
self.rpc_service.add(impl_kb_cummerbund.create_interactive_heatmap_de_genes,
name='kb_cummerbund.create_interactive_heatmap_de_genes',
types=[dict])
self.method_authentication['kb_cummerbund.create_interactive_heatmap_de_genes'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'MSSeedSupportServer'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_MSSeedSupportServer.getRastGenomeData,
name='MSSeedSupportServer.getRastGenomeData',
types=[dict])
self.method_authentication['MSSeedSupportServer.getRastGenomeData'] = 'none'
self.rpc_service.add(impl_MSSeedSupportServer.load_model_to_modelseed,
name='MSSeedSupportServer.load_model_to_modelseed',
types=[dict])
self.method_authentication['MSSeedSupportServer.load_model_to_modelseed'] = 'none'
self.rpc_service.add(impl_MSSeedSupportServer.list_rast_jobs,
name='MSSeedSupportServer.list_rast_jobs',
types=[dict])
self.method_authentication['MSSeedSupportServer.list_rast_jobs'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or "KBaseRNASeq"
self.userlog = log.log(
submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file(),
)
self.serverlog = log.log(
submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file(),
)
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_KBaseRNASeq.CallFastqc, name="KBaseRNASeq.CallFastqc", types=[dict])
self.method_authentication["KBaseRNASeq.CallFastqc"] = "required"
self.rpc_service.add(impl_KBaseRNASeq.BuildBowtie2Index, name="KBaseRNASeq.BuildBowtie2Index", types=[dict])
self.method_authentication["KBaseRNASeq.BuildBowtie2Index"] = "required"
self.rpc_service.add(impl_KBaseRNASeq.CallBowtie2, name="KBaseRNASeq.CallBowtie2", types=[dict])
self.method_authentication["KBaseRNASeq.CallBowtie2"] = "required"
self.rpc_service.add(impl_KBaseRNASeq.TophatCall, name="KBaseRNASeq.TophatCall", types=[dict])
self.method_authentication["KBaseRNASeq.TophatCall"] = "required"
self.rpc_service.add(impl_KBaseRNASeq.CufflinksCall, name="KBaseRNASeq.CufflinksCall", types=[dict])
self.method_authentication["KBaseRNASeq.CufflinksCall"] = "required"
self.rpc_service.add(impl_KBaseRNASeq.CuffmergeCall, name="KBaseRNASeq.CuffmergeCall", types=[dict])
self.method_authentication["KBaseRNASeq.CuffmergeCall"] = "required"
self.rpc_service.add(impl_KBaseRNASeq.CuffdiffCall, name="KBaseRNASeq.CuffdiffCall", types=[dict])
self.method_authentication["KBaseRNASeq.CuffdiffCall"] = "required"
self.rpc_service.add(impl_KBaseRNASeq.getAlignmentStats, name="KBaseRNASeq.getAlignmentStats", types=[dict])
self.method_authentication["KBaseRNASeq.getAlignmentStats"] = "required"
self.rpc_service.add(
impl_KBaseRNASeq.createExpressionHistogram, name="KBaseRNASeq.createExpressionHistogram", types=[dict]
)
self.method_authentication["KBaseRNASeq.createExpressionHistogram"] = "required"
self.rpc_service.add(impl_KBaseRNASeq.CallCummeRbund, name="KBaseRNASeq.CallCummeRbund", types=[dict])
self.method_authentication["KBaseRNASeq.CallCummeRbund"] = "required"
self.rpc_service.add(
impl_KBaseRNASeq.createExpressionSeries, name="KBaseRNASeq.createExpressionSeries", types=[dict]
)
self.method_authentication["KBaseRNASeq.createExpressionSeries"] = "required"
self.rpc_service.add(
impl_KBaseRNASeq.createExpressionMatrix, name="KBaseRNASeq.createExpressionMatrix", types=[dict]
)
self.method_authentication["KBaseRNASeq.createExpressionMatrix"] = "required"
self.auth_client = biokbase.nexus.Client(
config={"server": "nexus.api.globusonline.org", "verify_ssl": True, "client": None, "client_secret": None}
)
def __init__(self):
submod = get_service_name() or 'KBaseRNASeq'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_KBaseRNASeq.CreateRNASeqSampleSet,
name='KBaseRNASeq.CreateRNASeqSampleSet',
types=[dict])
self.method_authentication['KBaseRNASeq.CreateRNASeqSampleSet'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.BuildBowtie2Index,
name='KBaseRNASeq.BuildBowtie2Index',
types=[dict])
self.method_authentication['KBaseRNASeq.BuildBowtie2Index'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.GetFeaturesToGTF,
name='KBaseRNASeq.GetFeaturesToGTF',
types=[dict])
self.method_authentication['KBaseRNASeq.GetFeaturesToGTF'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.Bowtie2Call,
name='KBaseRNASeq.Bowtie2Call',
types=[dict])
self.method_authentication['KBaseRNASeq.Bowtie2Call'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.Hisat2Call,
name='KBaseRNASeq.Hisat2Call',
types=[dict])
self.method_authentication['KBaseRNASeq.Hisat2Call'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.TophatCall,
name='KBaseRNASeq.TophatCall',
types=[dict])
self.method_authentication['KBaseRNASeq.TophatCall'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.StringTieCall,
name='KBaseRNASeq.StringTieCall',
types=[dict])
self.method_authentication['KBaseRNASeq.StringTieCall'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.CufflinksCall,
name='KBaseRNASeq.CufflinksCall',
types=[dict])
self.method_authentication['KBaseRNASeq.CufflinksCall'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.CuffdiffCall,
name='KBaseRNASeq.CuffdiffCall',
types=[dict])
self.method_authentication['KBaseRNASeq.CuffdiffCall'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.DiffExpCallforBallgown,
name='KBaseRNASeq.DiffExpCallforBallgown',
types=[dict])
self.method_authentication['KBaseRNASeq.DiffExpCallforBallgown'] = 'required'
self.rpc_service.add(impl_KBaseRNASeq.status,
name='KBaseRNASeq.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'uniprotkb_keyword2go'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
def __init__(self):
submod = get_service_name() or "kb_cummerbund"
self.userlog = log.log(
submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file(),
)
self.serverlog = log.log(
submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file(),
)
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(
impl_kb_cummerbund.generate_cummerbund_plots, name="kb_cummerbund.generate_cummerbund_plots", types=[dict]
)
self.method_authentication["kb_cummerbund.generate_cummerbund_plots"] = "required"
self.rpc_service.add(
impl_kb_cummerbund.generate_cummerbund_plot2, name="kb_cummerbund.generate_cummerbund_plot2", types=[dict]
)
self.method_authentication["kb_cummerbund.generate_cummerbund_plot2"] = "required"
self.rpc_service.add(
impl_kb_cummerbund.create_expression_matrix, name="kb_cummerbund.create_expression_matrix", types=[dict]
)
self.method_authentication["kb_cummerbund.create_expression_matrix"] = "required"
self.rpc_service.add(
impl_kb_cummerbund.create_interactive_heatmap_de_genes,
name="kb_cummerbund.create_interactive_heatmap_de_genes",
types=[dict],
)
self.method_authentication["kb_cummerbund.create_interactive_heatmap_de_genes"] = "required"
self.rpc_service.add(
impl_kb_cummerbund.create_interactive_heatmap_de_genes_old,
name="kb_cummerbund.create_interactive_heatmap_de_genes_old",
types=[dict],
)
self.method_authentication["kb_cummerbund.create_interactive_heatmap_de_genes_old"] = "required"
self.rpc_service.add(impl_kb_cummerbund.status, name="kb_cummerbund.status", types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'HelloService'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.rpc_service.add(impl_HelloService.say_hello,
name='HelloService.say_hello',
types=[basestring])
def __init__(self, config):
#BEGIN_CONSTRUCTOR
if config == None:
# There needs to be a config for the server to work.
raise ValueError("__init__: A valid configuration was not provided. Check KB_DEPLOYMENT_CONFIG and KB_SERVICE_NAME environment variables.")
else:
self.config = config
# Create the work folder if it does not exist.
if not os.path.exists(self.config['work_folder_path']):
os.makedirs(self.config['work_folder_path'], 0775)
# Log info about the server configuration (need to create our own logger object since
# we do not have a context during initialization).
submod = os.environ.get('KB_SERVICE_NAME', 'CompressionBasedDistance')
mylog = log.log(submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, config=os.getenv('KB_DEPLOYMENT_CONFIG'))
mylog.log_message(log.INFO, 'Server started, version is '+VERSION)
configValues = 'shock_url='+self.config['shock_url']+', userandjobstate_url='+self.config['userandjobstate_url']
configValues += ', work_folder_path='+self.config['work_folder_path']+', num_pool_processes='+self.config['num_pool_processes']
mylog.log_message(log.INFO, configValues)
#END_CONSTRUCTOR
pass
def __init__(self):
submod = get_service_name() or 'HelloService3'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.rpc_service.add(impl_HelloService3.do_something,
name='HelloService3.do_something',
types=[])
self.rpc_service.add(impl_HelloService3.status,
name='HelloService3.status',
types=[dict])
def __init__(self):
submod = get_service_name() or 'NarrativeJobService'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_NarrativeJobService.run_app,
name='NarrativeJobService.run_app',
types=[dict])
self.method_authentication['NarrativeJobService.run_app'] = 'required'
self.rpc_service.add(impl_NarrativeJobService.compose_app,
name='NarrativeJobService.compose_app',
types=[dict])
self.method_authentication['NarrativeJobService.compose_app'] = 'required'
self.rpc_service.add(impl_NarrativeJobService.check_app_state,
name='NarrativeJobService.check_app_state',
types=[basestring])
self.method_authentication['NarrativeJobService.check_app_state'] = 'required'
self.rpc_service.add(impl_NarrativeJobService.suspend_app,
name='NarrativeJobService.suspend_app',
types=[basestring])
self.method_authentication['NarrativeJobService.suspend_app'] = 'required'
self.rpc_service.add(impl_NarrativeJobService.resume_app,
name='NarrativeJobService.resume_app',
types=[basestring])
self.method_authentication['NarrativeJobService.resume_app'] = 'required'
self.rpc_service.add(impl_NarrativeJobService.delete_app,
name='NarrativeJobService.delete_app',
types=[basestring])
self.method_authentication['NarrativeJobService.delete_app'] = 'required'
self.rpc_service.add(impl_NarrativeJobService.list_config,
name='NarrativeJobService.list_config',
types=[])
self.method_authentication['NarrativeJobService.list_config'] = 'optional'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
''' Initialize object.
@return Nothing
'''
# Create a logger.
submod = os.environ.get('KB_SERVICE_NAME', 'ProbabilisticAnnotation')
self.logger = log.log(submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, config=os.getenv('KB_DEPLOYMENT_CONFIG'))
def __init__(self):
submod = get_service_name() or 'poolcount'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_poolcount.run_poolcount,
name='poolcount.run_poolcount',
types=[dict])
self.method_authentication['poolcount.run_poolcount'] = 'required' # noqa
self.rpc_service.add(impl_poolcount.status,
name='poolcount.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'syujaContigFilter'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_syujaContigFilter.filter_contigs,
name='syujaContigFilter.filter_contigs',
types=[basestring, basestring])
self.method_authentication['syujaContigFilter.filter_contigs'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None})
def __init__(self):
submod = get_service_name() or 'landContigFilter'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_landContigFilter.filter_contigs,
name='landContigFilter.filter_contigs',
types=[dict])
self.method_authentication[
'landContigFilter.filter_contigs'] = 'required' # noqa
self.rpc_service.add(impl_landContigFilter.filter_contigs_max,
name='landContigFilter.filter_contigs_max',
types=[dict])
self.method_authentication[
'landContigFilter.filter_contigs_max'] = 'required' # noqa
self.rpc_service.add(impl_landContigFilter.assembly_metadata_report,
name='landContigFilter.assembly_metadata_report',
types=[dict])
self.method_authentication[
'landContigFilter.assembly_metadata_report'] = 'required' # noqa
self.rpc_service.add(impl_landContigFilter.status,
name='landContigFilter.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'AssemblyUtil'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_AssemblyUtil.get_assembly_as_fasta,
name='AssemblyUtil.get_assembly_as_fasta',
types=[dict])
self.method_authentication[
'AssemblyUtil.get_assembly_as_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.export_assembly_as_fasta,
name='AssemblyUtil.export_assembly_as_fasta',
types=[dict])
self.method_authentication[
'AssemblyUtil.export_assembly_as_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.save_assembly_from_fasta,
name='AssemblyUtil.save_assembly_from_fasta',
types=[dict])
self.method_authentication[
'AssemblyUtil.save_assembly_from_fasta'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyUtil.status,
name='AssemblyUtil.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'FamaProfiling'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_FamaProfiling.run_FamaReadProfiling,
name='FamaProfiling.run_FamaReadProfiling',
types=[dict])
self.method_authentication[
'FamaProfiling.run_FamaReadProfiling'] = 'required' # noqa
self.rpc_service.add(impl_FamaProfiling.run_FamaGenomeProfiling,
name='FamaProfiling.run_FamaGenomeProfiling',
types=[dict])
self.method_authentication[
'FamaProfiling.run_FamaGenomeProfiling'] = 'required' # noqa
self.rpc_service.add(impl_FamaProfiling.view_FamaFunctionalProfile,
name='FamaProfiling.view_FamaFunctionalProfile',
types=[dict])
self.method_authentication[
'FamaProfiling.view_FamaFunctionalProfile'] = 'required' # noqa
self.rpc_service.add(impl_FamaProfiling.status,
name='FamaProfiling.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'GenomeSearchUtil'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_GenomeSearchUtil.search,
name='GenomeSearchUtil.search',
types=[dict])
self.method_authentication[
'GenomeSearchUtil.search'] = 'optional' # noqa
self.rpc_service.add(impl_GenomeSearchUtil.search_region,
name='GenomeSearchUtil.search_region',
types=[dict])
self.method_authentication[
'GenomeSearchUtil.search_region'] = 'optional' # noqa
self.rpc_service.add(impl_GenomeSearchUtil.search_contigs,
name='GenomeSearchUtil.search_contigs',
types=[dict])
self.method_authentication[
'GenomeSearchUtil.search_contigs'] = 'optional' # noqa
self.rpc_service.add(impl_GenomeSearchUtil.status,
name='GenomeSearchUtil.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'kb_hmmer'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_kb_hmmer.HMMER_MSA_Search,
name='kb_hmmer.HMMER_MSA_Search',
types=[dict])
self.method_authentication[
'kb_hmmer.HMMER_MSA_Search'] = 'required' # noqa
self.rpc_service.add(impl_kb_hmmer.HMMER_Local_MSA_Group_Search,
name='kb_hmmer.HMMER_Local_MSA_Group_Search',
types=[dict])
self.method_authentication[
'kb_hmmer.HMMER_Local_MSA_Group_Search'] = 'required' # noqa
self.rpc_service.add(impl_kb_hmmer.HMMER_dbCAN_Search,
name='kb_hmmer.HMMER_dbCAN_Search',
types=[dict])
self.method_authentication[
'kb_hmmer.HMMER_dbCAN_Search'] = 'required' # noqa
self.rpc_service.add(impl_kb_hmmer.status,
name='kb_hmmer.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'WipeDev03'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_WipeDev03.wipe_dev03,
name='WipeDev03.wipe_dev03',
types=[])
self.method_authentication['WipeDev03.wipe_dev03'] = 'required'
self.rpc_service.add(impl_WipeDev03.shut_down_workspace,
name='WipeDev03.shut_down_workspace',
types=[])
self.method_authentication[
'WipeDev03.shut_down_workspace'] = 'required'
self.rpc_service.add(impl_WipeDev03.restart_workspace,
name='WipeDev03.restart_workspace',
types=[])
self.method_authentication['WipeDev03.restart_workspace'] = 'required'
self.auth_client = biokbase.nexus.Client(
config={
'server': 'nexus.api.globusonline.org',
'verify_ssl': False,
'client': None,
'client_secret': None
})
def __init__(self):
submod = get_service_name() or 'FakeObjectsForTests'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_FakeObjectsForTests.create_any_objects,
name='FakeObjectsForTests.create_any_objects',
types=[dict])
self.method_authentication[
'FakeObjectsForTests.create_any_objects'] = 'required' # noqa
self.rpc_service.add(impl_FakeObjectsForTests.create_fake_genomes,
name='FakeObjectsForTests.create_fake_genomes',
types=[dict])
self.method_authentication[
'FakeObjectsForTests.create_fake_genomes'] = 'required' # noqa
self.rpc_service.add(impl_FakeObjectsForTests.create_fake_reads,
name='FakeObjectsForTests.create_fake_reads',
types=[dict])
self.method_authentication[
'FakeObjectsForTests.create_fake_reads'] = 'required' # noqa
self.rpc_service.add(impl_FakeObjectsForTests.status,
name='FakeObjectsForTests.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'kb_Msuite'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.rpc_service.add(impl_kb_Msuite.status,
name='kb_Msuite.status',
types=[dict])
def __init__(self):
submod = get_service_name() or 'HelloService2'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.rpc_service.add(impl_HelloService2.say_hello,
name='HelloService2.say_hello',
types=[basestring])
def __init__(self):
submod = get_service_name() or 'ReadsUtils'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_ReadsUtils.validateFASTQ,
name='ReadsUtils.validateFASTQ',
types=[list])
self.method_authentication['ReadsUtils.validateFASTQ'] = 'required'
self.rpc_service.add(impl_ReadsUtils.upload_reads,
name='ReadsUtils.upload_reads',
types=[dict])
self.method_authentication['ReadsUtils.upload_reads'] = 'required'
self.rpc_service.add(impl_ReadsUtils.status,
name='ReadsUtils.status',
types=[dict])
self.auth_client = biokbase.nexus.Client(
config={
'server': 'nexus.api.globusonline.org',
'verify_ssl': True,
'client': None,
'client_secret': None
})
def __init__(self):
submod = get_service_name() or 'ClusterServicePy'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.rpc_service.add(impl_ClusterServicePy.estimate_k,
name='ClusterServicePy.estimate_k',
types=[dict, int, int, int, int, int])
self.rpc_service.add(
impl_ClusterServicePy.estimate_k_new,
name='ClusterServicePy.estimate_k_new',
types=[dict, int, int, basestring, int, float, int, int])
self.rpc_service.add(impl_ClusterServicePy.cluster_k_means,
name='ClusterServicePy.cluster_k_means',
types=[dict, int, int, int, int, basestring])
self.rpc_service.add(impl_ClusterServicePy.cluster_hierarchical,
name='ClusterServicePy.cluster_hierarchical',
types=[dict, basestring, basestring, float, int])
self.rpc_service.add(impl_ClusterServicePy.clusters_from_dendrogram,
name='ClusterServicePy.clusters_from_dendrogram',
types=[dict, basestring, float])
self.rpc_service.add(impl_ClusterServicePy.calc_cluster_qualities,
name='ClusterServicePy.calc_cluster_qualities',
types=[list])
def __init__(self):
submod = get_service_name() or 'condor_stats'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_condor_stats.queue_status,
name='condor_stats.queue_status',
types=[dict])
self.method_authentication[
'condor_stats.queue_status'] = 'required' # noqa
self.rpc_service.add(impl_condor_stats.job_status,
name='condor_stats.job_status',
types=[dict])
self.method_authentication[
'condor_stats.job_status'] = 'required' # noqa
self.rpc_service.add(impl_condor_stats.status,
name='condor_stats.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
self.setupCondorConfig()
print("ABOUT TO SET UP CONDOR COMPLETEs")
def __init__(self):
submod = get_service_name() or 'DifferentialExpressionUtils'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_DifferentialExpressionUtils.upload_differentialExpression,
name='DifferentialExpressionUtils.upload_differentialExpression',
types=[dict])
self.method_authentication['DifferentialExpressionUtils.upload_differentialExpression'] = 'required' # noqa
self.rpc_service.add(impl_DifferentialExpressionUtils.save_differential_expression_matrix_set,
name='DifferentialExpressionUtils.save_differential_expression_matrix_set',
types=[dict])
self.method_authentication['DifferentialExpressionUtils.save_differential_expression_matrix_set'] = 'required' # noqa
self.rpc_service.add(impl_DifferentialExpressionUtils.download_differentialExpression,
name='DifferentialExpressionUtils.download_differentialExpression',
types=[dict])
self.method_authentication['DifferentialExpressionUtils.download_differentialExpression'] = 'required' # noqa
self.rpc_service.add(impl_DifferentialExpressionUtils.export_differentialExpression,
name='DifferentialExpressionUtils.export_differentialExpression',
types=[dict])
self.method_authentication['DifferentialExpressionUtils.export_differentialExpression'] = 'required' # noqa
self.rpc_service.add(impl_DifferentialExpressionUtils.export_diff_expr_matrix_as_tsv,
name='DifferentialExpressionUtils.export_diff_expr_matrix_as_tsv',
types=[dict])
self.method_authentication['DifferentialExpressionUtils.export_diff_expr_matrix_as_tsv'] = 'required' # noqa
self.rpc_service.add(impl_DifferentialExpressionUtils.status,
name='DifferentialExpressionUtils.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'FeatureSetUtils'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(
impl_FeatureSetUtils.upload_featureset_from_diff_expr,
name='FeatureSetUtils.upload_featureset_from_diff_expr',
types=[dict])
self.method_authentication[
'FeatureSetUtils.upload_featureset_from_diff_expr'] = 'required' # noqa
self.rpc_service.add(
impl_FeatureSetUtils.calculate_average_expression_matrix,
name='FeatureSetUtils.calculate_average_expression_matrix',
types=[dict])
self.method_authentication[
'FeatureSetUtils.calculate_average_expression_matrix'] = 'required' # noqa
self.rpc_service.add(impl_FeatureSetUtils.status,
name='FeatureSetUtils.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'kb_cummerbund'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_kb_cummerbund.generate_cummerbund_plots,
name='kb_cummerbund.generate_cummerbund_plots',
types=[dict])
self.method_authentication['kb_cummerbund.generate_cummerbund_plots'] = 'required'
self.rpc_service.add(impl_kb_cummerbund.generate_cummerbund_plot2,
name='kb_cummerbund.generate_cummerbund_plot2',
types=[dict])
self.method_authentication['kb_cummerbund.generate_cummerbund_plot2'] = 'required'
self.rpc_service.add(impl_kb_cummerbund.create_expression_matrix,
name='kb_cummerbund.create_expression_matrix',
types=[dict])
self.method_authentication['kb_cummerbund.create_expression_matrix'] = 'required'
self.rpc_service.add(impl_kb_cummerbund.create_interactive_heatmap_de_genes,
name='kb_cummerbund.create_interactive_heatmap_de_genes',
types=[dict])
self.method_authentication['kb_cummerbund.create_interactive_heatmap_de_genes'] = 'required'
self.rpc_service.add(impl_kb_cummerbund.create_interactive_heatmap_de_genes_old,
name='kb_cummerbund.create_interactive_heatmap_de_genes_old',
types=[dict])
self.method_authentication['kb_cummerbund.create_interactive_heatmap_de_genes_old'] = 'required'
self.rpc_service.add(impl_kb_cummerbund.status,
name='kb_cummerbund.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'ProteinStructureUtils'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(
impl_ProteinStructureUtils.batch_import_pdbs_from_metafile,
name='ProteinStructureUtils.batch_import_pdbs_from_metafile',
types=[dict])
self.method_authentication[
'ProteinStructureUtils.batch_import_pdbs_from_metafile'] = 'required' # noqa
self.rpc_service.add(
impl_ProteinStructureUtils.export_pdb_structures,
name='ProteinStructureUtils.export_pdb_structures',
types=[dict])
self.method_authentication[
'ProteinStructureUtils.export_pdb_structures'] = 'required' # noqa
self.rpc_service.add(impl_ProteinStructureUtils.status,
name='ProteinStructureUtils.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'ConditionUtils'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_ConditionUtils.get_conditions,
name='ConditionUtils.get_conditions',
types=[dict])
self.method_authentication['ConditionUtils.get_conditions'] = 'required' # noqa
self.rpc_service.add(impl_ConditionUtils.file_to_condition_set,
name='ConditionUtils.file_to_condition_set',
types=[dict])
self.method_authentication['ConditionUtils.file_to_condition_set'] = 'required' # noqa
self.rpc_service.add(impl_ConditionUtils.condition_set_to_tsv_file,
name='ConditionUtils.condition_set_to_tsv_file',
types=[dict])
self.method_authentication['ConditionUtils.condition_set_to_tsv_file'] = 'required' # noqa
self.rpc_service.add(impl_ConditionUtils.export_condition_set_tsv,
name='ConditionUtils.export_condition_set_tsv',
types=[dict])
self.method_authentication['ConditionUtils.export_condition_set_tsv'] = 'required' # noqa
self.rpc_service.add(impl_ConditionUtils.export_condition_set_excel,
name='ConditionUtils.export_condition_set_excel',
types=[dict])
self.method_authentication['ConditionUtils.export_condition_set_excel'] = 'required' # noqa
self.rpc_service.add(impl_ConditionUtils.status,
name='ConditionUtils.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'annotation_ontology_api'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(
impl_annotation_ontology_api.get_annotation_ontology_events,
name='annotation_ontology_api.get_annotation_ontology_events',
types=[dict])
self.method_authentication[
'annotation_ontology_api.get_annotation_ontology_events'] = 'optional' # noqa
self.rpc_service.add(
impl_annotation_ontology_api.add_annotation_ontology_events,
name='annotation_ontology_api.add_annotation_ontology_events',
types=[dict])
self.method_authentication[
'annotation_ontology_api.add_annotation_ontology_events'] = 'optional' # noqa
self.rpc_service.add(impl_annotation_ontology_api.status,
name='annotation_ontology_api.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'ExpressionAPI'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(
impl_ExpressionAPI.get_differentialExpressionMatrixSet,
name='ExpressionAPI.get_differentialExpressionMatrixSet',
types=[dict])
self.method_authentication[
'ExpressionAPI.get_differentialExpressionMatrixSet'] = 'required' # noqa
self.rpc_service.add(
impl_ExpressionAPI.get_enhancedFilteredExpressionMatrix,
name='ExpressionAPI.get_enhancedFilteredExpressionMatrix',
types=[dict])
self.method_authentication[
'ExpressionAPI.get_enhancedFilteredExpressionMatrix'] = 'required' # noqa
self.rpc_service.add(impl_ExpressionAPI.status,
name='ExpressionAPI.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'MergeMetabolicAnnotations'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_MergeMetabolicAnnotations.import_annotations,
name='MergeMetabolicAnnotations.import_annotations',
types=[dict])
self.method_authentication['MergeMetabolicAnnotations.import_annotations'] = 'required' # noqa
self.rpc_service.add(impl_MergeMetabolicAnnotations.import_bulk_annotations,
name='MergeMetabolicAnnotations.import_bulk_annotations',
types=[dict])
self.method_authentication['MergeMetabolicAnnotations.import_bulk_annotations'] = 'required' # noqa
self.rpc_service.add(impl_MergeMetabolicAnnotations.compare_metabolic_annotations,
name='MergeMetabolicAnnotations.compare_metabolic_annotations',
types=[dict])
self.method_authentication['MergeMetabolicAnnotations.compare_metabolic_annotations'] = 'required' # noqa
self.rpc_service.add(impl_MergeMetabolicAnnotations.merge_metabolic_annotations,
name='MergeMetabolicAnnotations.merge_metabolic_annotations',
types=[dict])
self.method_authentication['MergeMetabolicAnnotations.merge_metabolic_annotations'] = 'required' # noqa
self.rpc_service.add(impl_MergeMetabolicAnnotations.run_MergeMetabolicAnnotations,
name='MergeMetabolicAnnotations.run_MergeMetabolicAnnotations',
types=[dict])
self.method_authentication['MergeMetabolicAnnotations.run_MergeMetabolicAnnotations'] = 'required' # noqa
self.rpc_service.add(impl_MergeMetabolicAnnotations.status,
name='MergeMetabolicAnnotations.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'MotifFinderMEME'
self.userlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(
submod, ip_address=True, authuser=True, module=True, method=True,
call_id=True, logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_MotifFinderMEME.find_motifs,
name='MotifFinderMEME.find_motifs',
types=[dict])
self.method_authentication['MotifFinderMEME.find_motifs'] = 'required' # noqa
self.rpc_service.add(impl_MotifFinderMEME.BuildFastaFromSequenceSet,
name='MotifFinderMEME.BuildFastaFromSequenceSet',
types=[dict])
self.method_authentication['MotifFinderMEME.BuildFastaFromSequenceSet'] = 'required' # noqa
self.rpc_service.add(impl_MotifFinderMEME.ExtractPromotersFromFeatureSetandDiscoverMotifs,
name='MotifFinderMEME.ExtractPromotersFromFeatureSetandDiscoverMotifs',
types=[dict])
self.method_authentication['MotifFinderMEME.ExtractPromotersFromFeatureSetandDiscoverMotifs'] = 'required' # noqa
self.rpc_service.add(impl_MotifFinderMEME.DiscoverMotifsFromFasta,
name='MotifFinderMEME.DiscoverMotifsFromFasta',
types=[dict])
self.method_authentication['MotifFinderMEME.DiscoverMotifsFromFasta'] = 'required' # noqa
self.rpc_service.add(impl_MotifFinderMEME.DiscoverMotifsFromSequenceSet,
name='MotifFinderMEME.DiscoverMotifsFromSequenceSet',
types=[dict])
self.method_authentication['MotifFinderMEME.DiscoverMotifsFromSequenceSet'] = 'required' # noqa
self.rpc_service.add(impl_MotifFinderMEME.status,
name='MotifFinderMEME.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'mccorkleNewReadUtilsTestPython'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(
impl_mccorkleNewReadUtilsTestPython.filter_contigs,
name='mccorkleNewReadUtilsTestPython.filter_contigs',
types=[dict])
self.method_authentication[
'mccorkleNewReadUtilsTestPython.filter_contigs'] = 'required'
self.rpc_service.add(
impl_mccorkleNewReadUtilsTestPython.upload_fastq,
name='mccorkleNewReadUtilsTestPython.upload_fastq',
types=[dict])
self.method_authentication[
'mccorkleNewReadUtilsTestPython.upload_fastq'] = 'required'
self.rpc_service.add(impl_mccorkleNewReadUtilsTestPython.status,
name='mccorkleNewReadUtilsTestPython.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def _log(self, level, message):
# Create a logger if this is the first time the method has been called.
if self.logger is None:
submod = os.environ.get('KB_SERVICE_NAME',
'CompressionBasedDistance')
self.logger = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
config=os.getenv('KB_DEPLOYMENT_CONFIG'))
# Log the message.
self.logger.log_message(level, message, self.context['client_ip'],
self.context['user_id'],
self.context['module'], self.context['method'],
self.context['call_id'])
return
def __init__(self, config):
#BEGIN_CONSTRUCTOR
if config == None:
# There needs to be a config for the server to work.
raise ValueError(
"__init__: A valid configuration was not provided. Check KB_DEPLOYMENT_CONFIG and KB_SERVICE_NAME environment variables."
)
else:
self.config = config
# Create the work folder if it does not exist.
if not os.path.exists(self.config['work_folder_path']):
os.makedirs(self.config['work_folder_path'], 0775)
# Log info about the server configuration (need to create our own logger object since
# we do not have a context during initialization).
submod = os.environ.get('KB_SERVICE_NAME', 'CompressionBasedDistance')
mylog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
config=os.getenv('KB_DEPLOYMENT_CONFIG'))
mylog.log_message(log.INFO, 'Server started, version is ' + VERSION)
configValues = 'shock_url=' + self.config[
'shock_url'] + ', userandjobstate_url=' + self.config[
'userandjobstate_url']
configValues += ', work_folder_path=' + self.config[
'work_folder_path'] + ', num_pool_processes=' + self.config[
'num_pool_processes']
mylog.log_message(log.INFO, configValues)
#END_CONSTRUCTOR
pass
def __init__(self):
submod = get_service_name() or 'AssemblyRAST'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_AssemblyRAST.run_kiki,
name='AssemblyRAST.run_kiki',
types=[dict])
self.method_authentication[
'AssemblyRAST.run_kiki'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_velvet,
name='AssemblyRAST.run_velvet',
types=[dict])
self.method_authentication[
'AssemblyRAST.run_velvet'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_miniasm,
name='AssemblyRAST.run_miniasm',
types=[dict])
self.method_authentication[
'AssemblyRAST.run_miniasm'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_spades,
name='AssemblyRAST.run_spades',
types=[dict])
self.method_authentication[
'AssemblyRAST.run_spades'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_idba,
name='AssemblyRAST.run_idba',
types=[dict])
self.method_authentication[
'AssemblyRAST.run_idba'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_megahit,
name='AssemblyRAST.run_megahit',
types=[dict])
self.method_authentication[
'AssemblyRAST.run_megahit'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_ray,
name='AssemblyRAST.run_ray',
types=[dict])
self.method_authentication['AssemblyRAST.run_ray'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_masurca,
name='AssemblyRAST.run_masurca',
types=[dict])
self.method_authentication[
'AssemblyRAST.run_masurca'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_a5,
name='AssemblyRAST.run_a5',
types=[dict])
self.method_authentication['AssemblyRAST.run_a5'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_a6,
name='AssemblyRAST.run_a6',
types=[dict])
self.method_authentication['AssemblyRAST.run_a6'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.run_arast,
name='AssemblyRAST.run_arast',
types=[dict])
self.method_authentication[
'AssemblyRAST.run_arast'] = 'required' # noqa
self.rpc_service.add(impl_AssemblyRAST.status,
name='AssemblyRAST.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'GenericsAPI'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_GenericsAPI.fetch_data,
name='GenericsAPI.fetch_data',
types=[dict])
self.method_authentication[
'GenericsAPI.fetch_data'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_matrix,
name='GenericsAPI.export_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.export_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.validate_data,
name='GenericsAPI.validate_data',
types=[dict])
self.method_authentication[
'GenericsAPI.validate_data'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.import_matrix_from_excel,
name='GenericsAPI.import_matrix_from_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.import_matrix_from_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.import_matrix_from_biom,
name='GenericsAPI.import_matrix_from_biom',
types=[dict])
self.method_authentication[
'GenericsAPI.import_matrix_from_biom'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.save_object,
name='GenericsAPI.save_object',
types=[dict])
self.method_authentication[
'GenericsAPI.save_object'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.search_matrix,
name='GenericsAPI.search_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.search_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.filter_matrix,
name='GenericsAPI.filter_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.filter_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.standardize_matrix,
name='GenericsAPI.standardize_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.standardize_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.file_to_attribute_mapping,
name='GenericsAPI.file_to_attribute_mapping',
types=[dict])
self.method_authentication[
'GenericsAPI.file_to_attribute_mapping'] = 'required' # noqa
self.rpc_service.add(
impl_GenericsAPI.update_matrix_attribute_mapping,
name='GenericsAPI.update_matrix_attribute_mapping',
types=[dict])
self.method_authentication[
'GenericsAPI.update_matrix_attribute_mapping'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.attribute_mapping_to_tsv_file,
name='GenericsAPI.attribute_mapping_to_tsv_file',
types=[dict])
self.method_authentication[
'GenericsAPI.attribute_mapping_to_tsv_file'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_attribute_mapping_tsv,
name='GenericsAPI.export_attribute_mapping_tsv',
types=[dict])
self.method_authentication[
'GenericsAPI.export_attribute_mapping_tsv'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_attribute_mapping_excel,
name='GenericsAPI.export_attribute_mapping_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.export_attribute_mapping_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_cluster_set_excel,
name='GenericsAPI.export_cluster_set_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.export_cluster_set_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_corr_matrix_excel,
name='GenericsAPI.export_corr_matrix_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.export_corr_matrix_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_pca_matrix_excel,
name='GenericsAPI.export_pca_matrix_excel',
types=[dict])
self.method_authentication[
'GenericsAPI.export_pca_matrix_excel'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.export_amplicon_set_tsv,
name='GenericsAPI.export_amplicon_set_tsv',
types=[dict])
self.method_authentication[
'GenericsAPI.export_amplicon_set_tsv'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.compute_correlation_matrix,
name='GenericsAPI.compute_correlation_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.compute_correlation_matrix'] = 'required' # noqa
self.rpc_service.add(
impl_GenericsAPI.compute_correlation_across_matrices,
name='GenericsAPI.compute_correlation_across_matrices',
types=[dict])
self.method_authentication[
'GenericsAPI.compute_correlation_across_matrices'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.build_network,
name='GenericsAPI.build_network',
types=[dict])
self.method_authentication[
'GenericsAPI.build_network'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.run_pca,
name='GenericsAPI.run_pca',
types=[dict])
self.method_authentication['GenericsAPI.run_pca'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.view_matrix,
name='GenericsAPI.view_matrix',
types=[dict])
self.method_authentication[
'GenericsAPI.view_matrix'] = 'required' # noqa
self.rpc_service.add(impl_GenericsAPI.status,
name='GenericsAPI.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'kb_ea_utils'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_kb_ea_utils.get_fastq_ea_utils_stats,
name='kb_ea_utils.get_fastq_ea_utils_stats',
types=[dict])
self.method_authentication[
'kb_ea_utils.get_fastq_ea_utils_stats'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.run_app_fastq_ea_utils_stats,
name='kb_ea_utils.run_app_fastq_ea_utils_stats',
types=[dict])
self.method_authentication[
'kb_ea_utils.run_app_fastq_ea_utils_stats'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.get_ea_utils_stats,
name='kb_ea_utils.get_ea_utils_stats',
types=[dict])
self.method_authentication[
'kb_ea_utils.get_ea_utils_stats'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.calculate_fastq_stats,
name='kb_ea_utils.calculate_fastq_stats',
types=[dict])
self.method_authentication[
'kb_ea_utils.calculate_fastq_stats'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.run_Fastq_Multx,
name='kb_ea_utils.run_Fastq_Multx',
types=[dict])
self.method_authentication[
'kb_ea_utils.run_Fastq_Multx'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.run_Fastq_Join,
name='kb_ea_utils.run_Fastq_Join',
types=[dict])
self.method_authentication[
'kb_ea_utils.run_Fastq_Join'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.exec_Fastq_Join,
name='kb_ea_utils.exec_Fastq_Join',
types=[dict])
self.method_authentication[
'kb_ea_utils.exec_Fastq_Join'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.exec_Fastq_Join_OneLibrary,
name='kb_ea_utils.exec_Fastq_Join_OneLibrary',
types=[dict])
self.method_authentication[
'kb_ea_utils.exec_Fastq_Join_OneLibrary'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.exec_Determine_Phred,
name='kb_ea_utils.exec_Determine_Phred',
types=[dict])
self.method_authentication[
'kb_ea_utils.exec_Determine_Phred'] = 'required' # noqa
self.rpc_service.add(impl_kb_ea_utils.status,
name='kb_ea_utils.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def __init__(self):
submod = get_service_name() or 'SampleService'
self.userlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
changecallback=self.logcallback,
config=get_config_file())
self.serverlog = log.log(submod,
ip_address=True,
authuser=True,
module=True,
method=True,
call_id=True,
logfile=self.userlog.get_log_file())
self.serverlog.set_log_level(6)
self.rpc_service = JSONRPCServiceCustom()
self.method_authentication = dict()
self.rpc_service.add(impl_SampleService.create_sample,
name='SampleService.create_sample',
types=[dict])
self.method_authentication[
'SampleService.create_sample'] = 'required' # noqa
self.rpc_service.add(impl_SampleService.get_sample,
name='SampleService.get_sample',
types=[dict])
self.method_authentication[
'SampleService.get_sample'] = 'required' # noqa
self.rpc_service.add(impl_SampleService.get_sample_acls,
name='SampleService.get_sample_acls',
types=[dict])
self.method_authentication[
'SampleService.get_sample_acls'] = 'required' # noqa
self.rpc_service.add(impl_SampleService.replace_sample_acls,
name='SampleService.replace_sample_acls',
types=[dict])
self.method_authentication[
'SampleService.replace_sample_acls'] = 'required' # noqa
self.rpc_service.add(
impl_SampleService.get_metadata_key_static_metadata,
name='SampleService.get_metadata_key_static_metadata',
types=[dict])
self.method_authentication[
'SampleService.get_metadata_key_static_metadata'] = 'none' # noqa
self.rpc_service.add(impl_SampleService.create_data_link,
name='SampleService.create_data_link',
types=[dict])
self.method_authentication[
'SampleService.create_data_link'] = 'required' # noqa
self.rpc_service.add(impl_SampleService.expire_data_link,
name='SampleService.expire_data_link',
types=[dict])
self.method_authentication[
'SampleService.expire_data_link'] = 'required' # noqa
self.rpc_service.add(impl_SampleService.get_data_links_from_sample,
name='SampleService.get_data_links_from_sample',
types=[dict])
self.method_authentication[
'SampleService.get_data_links_from_sample'] = 'required' # noqa
self.rpc_service.add(impl_SampleService.get_data_links_from_data,
name='SampleService.get_data_links_from_data',
types=[dict])
self.method_authentication[
'SampleService.get_data_links_from_data'] = 'required' # noqa
self.rpc_service.add(impl_SampleService.get_sample_via_data,
name='SampleService.get_sample_via_data',
types=[dict])
self.method_authentication[
'SampleService.get_sample_via_data'] = 'required' # noqa
self.rpc_service.add(impl_SampleService.status,
name='SampleService.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
