IGF-HPC-Airflow/dags/dag14_crick_seqrun_transfer.py

import argparse
from datetime import timedelta
from airflow.models import DAG,Variable
from airflow.utils.dates import days_ago
from airflow.contrib.operators.ssh_operator import SSHOperator
from airflow.contrib.hooks.ssh_hook import SSHHook
from airflow.operators.python_operator import PythonOperator
from igf_airflow.utils.dag14_crick_seqrun_transfer_utils import check_and_transfer_run_func
from igf_airflow.utils.dag14_crick_seqrun_transfer_utils import extract_tar_file_func

FTP_SEQRUN_SERVER = Variable.get('crick_ftp_seqrun_hostname')
FTP_CONFIG_FILE = Variable.get('crick_ftp_config_file')
SEQRUN_BASE_PATH = Variable.get('seqrun_base_path')
HPC_SEQRUN_BASE_PATH = Variable.get('hpc_seqrun_path')

args = {
    'owner': 'airflow',
    'start_date': days_ago(2),
    'retries': 1,
    'retry_delay': timedelta(minutes=5),
    'provide_context': True,
    'email_on_failure': False,
    'email_on_retry': False,
    'catchup': False,
    'max_active_runs': 1,
}

## SSH HOOK
orwell_ssh_hook = \
  SSHHook(
    key_file=Variable.get('hpc_ssh_key_file'),
    username=Variable.get('hpc_user'),
    remote_host=Variable.get('orwell_server_hostname'))

dag = \
  DAG(
    dag_id='dag14_crick_seqrun_transfer',
    schedule_interval=None,
    default_args=args,
    tags=['ftp', 'hpc', 'orwell'])


with dag:
  ## TASK
  check_and_transfer_run = \
    PythonOperator(
      task_id='check_and_transfer_run',
      dag=dag,
      pool='crick_ftp_pool',
      queue='hpc_4G',
      params={'ftp_seqrun_server': FTP_SEQRUN_SERVER,
             'hpc_seqrun_base_path': HPC_SEQRUN_BASE_PATH,
             'ftp_config_file': FTP_CONFIG_FILE},
      python_callable=check_and_transfer_run_func)
  ## TASK
  extract_tar_file = \
    PythonOperator(
      task_id='extract_tar_file',
      dag=dag,
      queue='hpc_4G',
      params={'hpc_seqrun_base_path': HPC_SEQRUN_BASE_PATH},
      python_callable=extract_tar_file_func)
  #check_and_transfer_run = \
  #  SSHOperator(
  #    task_id='check_and_transfer_run',
  #    dag=dag,
  #    pool='crick_ftp_pool',
  #    ssh_hook=orwell_ssh_hook,
  #    do_xcom_push=False,
  #    queue='hpc_4G',
  #    params={'ftp_seqrun_server': FTP_SEQRUN_SERVER,
  #            'seqrun_base_path': SEQRUN_BASE_PATH,
  #            'ftp_config_file': FTP_CONFIG_FILE},
  #    command="""
  #      source /home/igf/igf_code/airflow/env.sh;
  #      python /home/igf/igf_code/airflow/data-management-python/scripts/ftp_seqrun_transfer/transfer_seqrun_from_crick.py \
  #        -f {{ params.ftp_seqrun_server }} \
  #        -s {{ dag_run.conf["seqrun_id"] }} \
  #        -d {{ params.seqrun_base_path }} \
  #        -c {{ params.ftp_config_file }}
  #      """)
  ## TASK
  #extract_tar_file = \
  #  SSHOperator(
  #    task_id='extract_tar_file',
  #    dag=dag,
  #    pool='orwell_exe_pool',
  #    ssh_hook=orwell_ssh_hook,
  #    do_xcom_push=False,
  #    queue='hpc_4G',
  #    params={'seqrun_base_path': SEQRUN_BASE_PATH},
  #    command="""
  #    cd {{ params.seqrun_base_path }};
  #    if [ -d {{ dag_run.conf["seqrun_id"] }} ];
  #    then
  #      echo "Seqrun dir exists";
  #      exit 1;
  #    else
  #      mkdir -p {{ dag_run.conf["seqrun_id"] }};
  #      tar \
  #        --no-same-owner \
  #        --no-same-permissions \
  #        --owner=igf \
  #        -xzf {{ dag_run.conf["seqrun_id"] }}.tar.gz -C {{ dag_run.conf["seqrun_id"] }}
  #    fi
  #    """
  #  )
  ## PIPELINE
  check_and_transfer_run >> extract_tar_file