def __init__(self):
submod = get_service_name() or 'kb_fastqc'
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_fastqc.runFastQC,
name='kb_fastqc.runFastQC',
types=[dict])
self.method_authentication['kb_fastqc.runFastQC'] = 'required' # noqa
self.rpc_service.add(impl_kb_fastqc.status,
name='kb_fastqc.status',
types=[dict])
authurl = config.get(AUTH) if config else None
self.auth_client = _KBaseAuth(authurl)
def setUpClass(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_fastqc'):
cls.cfg[nameval[0]] = nameval[1]
authServiceUrl = cls.cfg.get(
'auth-service-url',
"https://kbase.us/services/authorization/Sessions/Login")
auth_client = _KBaseAuth(authServiceUrl)
user_id = auth_client.get_user(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':
token,
'user_id':
user_id,
'provenance': [{
'service': 'kb_fastqc',
'method': 'please_never_use_it_in_production',
'method_params': []
}],
'authenticated':
1
})
cls.wsURL = cls.cfg['workspace-url']
cls.wsClient = workspaceService(cls.wsURL, token=token)
cls.serviceImpl = kb_fastqc(cls.cfg)
#retrieve and setup test files
test_fq_filename = "test_1.fastq.gz"
output = subprocess.check_output([
"curl", "-o", test_fq_filename,
"http://bioseed.mcs.anl.gov/~seaver/Files/Sample_Reads/WT1_S1_L001_R2_001.fastq.gz"
])
cls.large_fq_test_file1 = os.path.join(cls.cfg['scratch'],
test_fq_filename)
shutil.copy(test_fq_filename, cls.large_fq_test_file1)
fq_filename = "interleaved.fq"
cls.small_fq_test_file2 = os.path.join(cls.cfg['scratch'], fq_filename)
shutil.copy(os.path.join("data", fq_filename), cls.small_fq_test_file2)