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)