def main():
args = parser.parse_args()
# Check and sanitize user input
args = check_input(args)
# Create logfile to track the analysis, overwrite it if it exist ("w+" mode)
time_stamp = time.strftime("%Y%m%d-%H%M%S")
logfile = os.path.join(args.outpath, f"{time_stamp}_{args.outname}_logfile_temp.out")
logger(logfile, w_mode="w+")
# Record executed command
command = " ".join(sys.argv)
print(f"\n{command}\n", flush=True)
# Run analysis
try:
transfix_gtf = transfix_main(args.gtf, args.fasta, args.outpath, args.outname,
iter_th=args.iter_th, chimeric=args.chimeric)
# Annotate additional features (UTR, start/stop codons)
_ = add_features_to_gtf(transfix_gtf)
except SystemExit as err:
# Valid for python 3.5+
print("".join(traceback.TracebackException.from_exception(err).format()))
except Exception as err:
print("".join(traceback.TracebackException.from_exception(err).format()))
sys.exit(f"{err}")
clean_log(logfile)
def __init__(self,parameters,audit_entires):
self.parameters = parameters
self.audit_entires = audit_entires
self.process_cmd_txt = []
self.logger = logger(self.parameters["log_dir"],self.parameters["log_file"],self.__class__.__name__).get()
self.logger.info("ParameterEvaluation API Started")
def __init__(self, parameters):
self.parameters = parameters
self.logger = logger(self.parameters["log_dir"],
self.parameters["log_file"],
'SQLExecutor:' + self.__class__.__name__).get()
self.logger.info("ParameterEvaluation API Started")
def __init__(self, parameters):
self.parameters = parameters
self.cmd = []
self.logger = logger(self.parameters["log_dir"],
self.parameters["log_file"], 'IICSCTaskRunner:' +
self.__class__.__name__).get()
self.logger.info("Command Runner API has Started")
def __init__(self, parameters):
self.parameters = parameters
self.logger = logger(self.parameters["log_dir"],
self.parameters["log_file"],
'BCPRunner:' + self.__class__.__name__).get()
self.logger.info("Session API Started")
# Decrypting connection info using gpg utility
self.DB_CONN_NM = self.parameters["DB_CONN_NM"]
# gpg_cmd = "gpg --yes --batch --output - --passphrase=%s --decrypt %s | grep %s" % (base64.b64decode(settings.GPG_PASSPHRASE).decode(),settings.GPG_CONN_FILE,self.DB_CONN_NM)
gpg_cmd = "gpg --yes --batch --output - --passphrase=%s --decrypt %s" % (
base64.b64decode(
settings.GPG_PASSPHRASE).decode(), settings.GPG_CONN_FILE)
grep_cmd = "grep %s" % self.DB_CONN_NM
self.logger.info("gpg command to be executed : %s" % gpg_cmd)
try:
process_connstr = subprocess.Popen(shlex.split(gpg_cmd),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
process_conndtl = subprocess.Popen(shlex.split(grep_cmd),
stdin=process_connstr.stdout,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
conn_dtl, stderr = process_conndtl.communicate()
if len(conn_dtl.strip()) == 0:
self.logger.error(
"Connection Details of CONN_NM are not part of entry. Please give entry"
)
raise Exception(
"Connection Details of CONN_NM are not part of entry. Please give entry"
)
conn_info = conn_dtl.decode().split("|")
self.DB_CONN_NM = conn_info[0]
self.SERVER_HOST = conn_info[1]
self.SERVER_PORT = conn_info[2]
self.DB_NM = conn_info[3]
self.SCH_NM = conn_info[4]
self.USER_NM = conn_info[5]
self.PASS_TX = conn_info[6]
except Exception as err:
self.logger.error("Error reading or decrypting connection file")
self.logger.error("Error stacktrace : %s" % err)
sys.exit(1)
self.logger.info("Audit Database connection name : %s" %
(self.DB_CONN_NM))
self.logger.info("Audit Database Server URL : %s" %
(self.SERVER_HOST))
self.logger.info("Audit Database Server Port : %s" %
(self.SERVER_PORT))
self.logger.info("Audit Database name : %s" % (self.DB_NM))
self.logger.info("Audit Database Schema name : %s" % (self.SCH_NM))
self.logger.info("Audit Database User name : %s" % (self.USER_NM))
def __init__(self, parameters, audit_entires, session):
self.parameters = parameters
self.audit_entires = audit_entires
self.session = session # added to handle checkpoints
self.process_cmd_txt = []
self.logger = logger(self.parameters["log_dir"],
self.parameters["log_file"],
self.__class__.__name__).get()
self.logger.info("CommandRunner API Started")
def __init__(self, parameters):
self.parameters = parameters
self.logger = logger(self.parameters["log_dir"],
self.parameters["log_file"], 'IICSCTaskRunner:' +
self.__class__.__name__).get()
self.logger.info("Parameter file creation Started")
def __init__(self, parameters):
#Import logger
self.parameters = parameters
self.logger = logger(self.parameters["log_dir"],
self.parameters["log_file"],
self.__class__.__name__).get()
self.logger.info("Session API Started")
#Decrypting connection info using gpg utility
self.DB_ADT_CONN_NM = settings.DB_ADT_CONN_NM
#gpg_cmd = "gpg --yes --batch --output - --passphrase=%s --decrypt %s | grep %s" % (base64.b64decode(settings.GPG_PASSPHRASE).decode(),settings.GPG_CONN_FILE,self.DB_ADT_CONN_NM)
gpg_cmd = "gpg --yes --batch --output - --passphrase=%s --decrypt %s" % (
base64.b64decode(
settings.GPG_PASSPHRASE).decode(), settings.GPG_CONN_FILE)
grep_cmd = "grep %s" % settings.DB_ADT_CONN_NM
self.logger.info("gpg command to be executed : %s" % gpg_cmd)
try:
process_connstr = subprocess.Popen(shlex.split(gpg_cmd),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
process_conndtl = subprocess.Popen(shlex.split(grep_cmd),
stdin=process_connstr.stdout,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
conn_dtl, stderr = process_conndtl.communicate()
if len(conn_dtl.strip()) == 0:
self.logger.error(
"Connection Details of CONN_NM are not part of entry. Please give entry"
)
raise Exception(
"Connection Details of CONN_NM are not part of entry. Please give entry"
)
conn_info = conn_dtl.decode().split("|")
self.DB_ADT_CONN_NM = conn_info[0]
self.SERVER_HOST = conn_info[1]
self.SERVER_PORT = conn_info[2]
self.ADT_DB_NM = conn_info[3]
self.ADT_SCH_NM = conn_info[4]
self.USER_NM = conn_info[5]
self.PASS_TX = conn_info[6]
except Exception as err:
self.logger.error("Error reading or decrypting connection file")
self.logger.error("Error stacktrace : %s" % err)
sys.exit(1)
# self.DB_ADT_CONN_NM = settings.DB_ADT_CONN_NM
# self.SERVER_HOST = settings.SERVER_HOST
# self.SERVER_PORT = settings.SERVER_PORT
# self.ADT_DB_NM = settings.ADT_DB_NM
# self.ADT_SCH_NM = settings.ADT_SCH_NM
# self.USER_NM = settings.USER_NM
# self.PASS_TX = base64.b64decode(settings.PASS_TX).decode() #settings.PASS_TX
self.logger.info("Audit Database connection name : %s" %
(self.DB_ADT_CONN_NM))
self.logger.info("Audit Database Server URL : %s" %
(self.SERVER_HOST))
self.logger.info("Audit Database Server Port : %s" %
(self.SERVER_PORT))
self.logger.info("Audit Database name : %s" % (self.ADT_DB_NM))
self.logger.info("Audit Database Schema name : %s" % (self.ADT_SCH_NM))
self.logger.info("Audit Database User name : %s" % (self.USER_NM))
self.logger.info("Creating a Session to Audit Database")
try:
connection_str = 'Driver={ODBC Driver 17 for SQL Server};Server=tcp:' + self.SERVER_HOST + ',' + self.SERVER_PORT + ';Database=' + self.ADT_DB_NM + ';Uid=' + self.USER_NM + '@' + self.SERVER_HOST.split(
"."
)[0] + ';Pwd=' + self.PASS_TX + ';Encrypt=yes;TrustServerCertificate=no;Connection Timeout=30;'
connection = pyodbc.connect(connection_str)
self.cursor = connection.cursor()
if self.cursor is not None:
self.logger.info("Cursor object created successfully")
self.logger.info(
self.cursor.execute("SELECT @@VERSION;").fetchone())
except Exception as err:
self.logger.error(
"Error while creating database connection. Please check connection entries"
)
self.logger.error("Error Stacktrace : %s" % (err))
sys.exit(1)
def __init__(self,parameters):
self.parameters = parameters
# self.logger = logger(self.parameters["log_dir"], self.parameters["log_file"], self.__class__.__name__).get()
self.logger = logger(self.parameters["log_dir"], self.parameters["log_file"],'BCPRunner:'+self.__class__.__name__).get()
self.logger.info("BCP Runner Started")