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)
