def setUpClass(cls): cls.token = environ.get('KB_AUTH_TOKEN', None) config_file = environ.get('KB_DEPLOYMENT_CONFIG', None) cls.cfg = {} config = ConfigParser() config.read(config_file) for nameval in config.items('kb_uploadmethods'): cls.cfg[nameval[0]] = nameval[1] authServiceUrl = cls.cfg.get('auth-service-url', "https://kbase.us/services/authorization/Sessions/Login") auth_client = _KBaseAuth(authServiceUrl) cls.user_id = auth_client.get_user(cls.token) # WARNING: don't call any logging methods on the context object, # it'll result in a NoneType error cls.ctx = MethodContext(None) cls.ctx.update({'token': cls.token, 'user_id': cls.user_id, 'provenance': [ {'service': 'kb_uploadmethods', 'method': 'please_never_use_it_in_production', 'method_params': [] }], 'authenticated': 1}) cls.wsURL = cls.cfg['workspace-url'] cls.wsClient = workspaceService(cls.wsURL, token=cls.token) cls.serviceImpl = kb_uploadmethods(cls.cfg) cls.dfu = DataFileUtil(os.environ['SDK_CALLBACK_URL'], token=cls.token) cls.scratch = cls.cfg['scratch'] cls.shockURL = cls.cfg['shock-url']
def __init__(self): submod = get_service_name() or 'kb_uploadmethods' 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_uploadmethods.upload_fastq_file, name='kb_uploadmethods.upload_fastq_file', types=[dict]) self.method_authentication[ 'kb_uploadmethods.upload_fastq_file'] = 'required' # noqa self.rpc_service.add(impl_kb_uploadmethods.status, name='kb_uploadmethods.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_uploadmethods' 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_uploadmethods.upload_fastq_file, name='kb_uploadmethods.upload_fastq_file', types=[dict]) self.method_authentication[ 'kb_uploadmethods.upload_fastq_file'] = 'required' # noqa self.rpc_service.add(impl_kb_uploadmethods.upload_fasta_gff_file, name='kb_uploadmethods.upload_fasta_gff_file', types=[dict]) self.method_authentication[ 'kb_uploadmethods.upload_fasta_gff_file'] = 'required' # noqa self.rpc_service.add(impl_kb_uploadmethods.unpack_staging_file, name='kb_uploadmethods.unpack_staging_file', types=[dict]) self.method_authentication[ 'kb_uploadmethods.unpack_staging_file'] = 'required' # noqa self.rpc_service.add(impl_kb_uploadmethods.unpack_web_file, name='kb_uploadmethods.unpack_web_file', types=[dict]) self.method_authentication[ 'kb_uploadmethods.unpack_web_file'] = 'required' # noqa self.rpc_service.add( impl_kb_uploadmethods.import_genbank_from_staging, name='kb_uploadmethods.import_genbank_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_genbank_from_staging'] = 'required' # noqa self.rpc_service.add(impl_kb_uploadmethods.import_sra_from_staging, name='kb_uploadmethods.import_sra_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_sra_from_staging'] = 'required' # noqa self.rpc_service.add(impl_kb_uploadmethods.import_sra_from_web, name='kb_uploadmethods.import_sra_from_web', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_sra_from_web'] = 'required' # noqa self.rpc_service.add( impl_kb_uploadmethods.import_fasta_as_assembly_from_staging, name='kb_uploadmethods.import_fasta_as_assembly_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_fasta_as_assembly_from_staging'] = 'required' # noqa self.rpc_service.add( impl_kb_uploadmethods.import_tsv_as_media_from_staging, name='kb_uploadmethods.import_tsv_as_media_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_tsv_as_media_from_staging'] = 'required' # noqa self.rpc_service.add( impl_kb_uploadmethods.import_excel_as_media_from_staging, name='kb_uploadmethods.import_excel_as_media_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_excel_as_media_from_staging'] = 'required' # noqa self.rpc_service.add( impl_kb_uploadmethods.import_tsv_or_excel_as_media_from_staging, name='kb_uploadmethods.import_tsv_or_excel_as_media_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_tsv_or_excel_as_media_from_staging'] = 'required' # noqa self.rpc_service.add( impl_kb_uploadmethods.import_file_as_fba_model_from_staging, name='kb_uploadmethods.import_file_as_fba_model_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_file_as_fba_model_from_staging'] = 'required' # noqa self.rpc_service.add( impl_kb_uploadmethods.import_tsv_as_expression_matrix_from_staging, name= 'kb_uploadmethods.import_tsv_as_expression_matrix_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_tsv_as_expression_matrix_from_staging'] = 'required' # noqa self.rpc_service.add(impl_kb_uploadmethods.import_reads_from_staging, name='kb_uploadmethods.import_reads_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_reads_from_staging'] = 'required' # noqa self.rpc_service.add( impl_kb_uploadmethods.import_tsv_as_phenotype_set_from_staging, name='kb_uploadmethods.import_tsv_as_phenotype_set_from_staging', types=[dict]) self.method_authentication[ 'kb_uploadmethods.import_tsv_as_phenotype_set_from_staging'] = 'required' # noqa self.rpc_service.add(impl_kb_uploadmethods.status, name='kb_uploadmethods.status', types=[dict]) authurl = config.get(AUTH) if config else None self.auth_client = _KBaseAuth(authurl)