def check_status(ctx, projectid, snic_api_credentials=None, statusdb_config=None):
"""In grus delivery mode checks the status of an onggoing delivery
"""
for pid in projectid:
if statusdb_config == None:
logger.error("--statusdb-config or env variable $STATUS_DB_CONFIG need to be set to perform GRUS delivery")
return 1
load_yaml_config(statusdb_config.name)
if snic_api_credentials == None:
logger.error("--snic-api-credentials or env variable $SNIC_API_STOCKHOLM need to be set to perform GRUS delivery")
return 1
load_yaml_config(snic_api_credentials.name)
d = _deliver_grus.GrusProjectDeliverer(
pid,
**ctx.parent.params)
d.check_mover_delivery_status()
def cli(ctx, config_file):
""" Tool for the Automation of Storage and Analyses """
ctx.obj = {}
config = conf.load_yaml_config(config_file.name)
log_file = config.get('log', {}).get('file', None)
if log_file:
level = config.get('log').get('log_level', 'INFO')
taca.log.init_logger_file(log_file, level)
logger.debug('starting up CLI')
def cli(ctx, config_file):
""" Tool for the Automation of Storage and Analyses """
ctx.obj = {}
config = conf.load_yaml_config(config_file)
log_file = config.get('log', {}).get('file', None)
if log_file:
level = config.get('log').get('log_level', 'INFO')
taca.log.init_logger_file(log_file, level)
logger.debug('starting up CLI')
def test_load_yaml_config(self):
"""Load a yaml config file"""
got_config_data = config.load_yaml_config(
'data/taca_test_cfg_minimal.yaml')
expexted_config_data = {
'statusdb': {
'url': 'url',
'username': '******',
'password': '******',
'port': 'port'
},
'log': {
'file': 'data/taca.log'
}
}
self.assertEqual(expexted_config_data, got_config_data)
with self.assertRaises(IOError):
missing_config_data = config.load_yaml_config(
'data/missing_file.yaml)')
def project(ctx, projectid, snic_api_credentials=None, statusdb_config=None, order_portal=None, pi_email=None, sensitive=True, hard_stage_only=False, add_user=None, fc_delivery=False):
""" Deliver the specified projects to the specified destination
"""
for pid in projectid:
if not ctx.parent.params['cluster']: # Soft stage case
d = _deliver.ProjectDeliverer(
pid,
**ctx.parent.params)
elif ctx.parent.params['cluster'] == 'grus': # Hard stage and deliver
if statusdb_config == None:
logger.error("--statusdb-config or env variable $STATUS_DB_CONFIG need to be set to perform GRUS delivery")
return 1
load_yaml_config(statusdb_config.name)
if snic_api_credentials == None:
logger.error("--snic-api-credentials or env variable $SNIC_API_STOCKHOLM need to be set to perform GRUS delivery")
return 1
load_yaml_config(snic_api_credentials.name)
if order_portal == None:
logger.error("--order-portal or env variable $ORDER_PORTAL need to be set to perform GRUS delivery")
return 1
load_yaml_config(order_portal.name)
d = _deliver_grus.GrusProjectDeliverer(
projectid=pid,
pi_email=pi_email,
sensitive=sensitive,
hard_stage_only=hard_stage_only,
add_user=list(set(add_user)),
fcid=fc_delivery,
**ctx.parent.params)
if fc_delivery:
_exec_fn(d, d.deliver_run_folder)
else:
_exec_fn(d, d.deliver_project)
import shutil
import tempfile
import unittest
import csv
from datetime import datetime
from taca.analysis.analysis import *
from taca.illumina.Runs import Run
from taca.illumina.HiSeqX_Runs import HiSeqX_Run
from taca.utils import config as conf
# This is only run if TACA is called from the CLI, as this is a test, we need to
# call it explicitely
CONFIG = conf.load_yaml_config('data/taca_test_cfg.yaml')
def processing_status(run_dir):
demux_dir = os.path.join(run_dir, 'Demultiplexing')
if not os.path.exists(demux_dir):
return 'TO_START'
elif os.path.exists(os.path.join(demux_dir, 'Stats', 'DemultiplexingStats.xml')):
return 'COMPLETED'
else:
return 'IN_PROGRESS'
class TestTracker(unittest.TestCase):
""" analysis.py script tests
"""
@classmethod
def setUpClass(self):
#!/usr/bin/env python
import os
import shutil
import tempfile
import unittest
import mock
from datetime import datetime
from taca.cleanup import cleanup
from taca.utils import config as conf
CONFIG = conf.load_yaml_config('data/taca_test_cfg_cleanup.yaml')
class TestCleanup(unittest.TestCase):
"""Tests for TACA Cleanup module."""
@mock.patch('taca.cleanup.cleanup.shutil.move')
@mock.patch('taca.cleanup.cleanup.os.listdir')
def test_cleanup_nas(self, mock_listdir, mock_move):
"""Locate and move old data on NAS."""
seconds = 1
run = '190201_A00621_0032_BHHFCFDSXX'
mock_listdir.return_value = [run]
cleanup.cleanup_nas(seconds)
mock_move.assert_called_once_with(run, 'nosync')
@mock.patch('taca.cleanup.cleanup.shutil.rmtree')
@mock.patch('taca.cleanup.cleanup.os.listdir')
def test_cleanup_processing(self, mock_listdir, mock_rmtree):
#!/usr/bin/env python
import os
import shutil
import unittest
from datetime import datetime
from taca.analysis.analysis import *
from taca.illumina import Run
from taca.utils import config
# This is only run if TACA is called from the CLI, as this is a test, we need to
# call it explicitely
config.load_yaml_config(os.path.join(os.environ.get('HOME'), '.taca/taca.yaml'))
def processing_status(run_dir):
demux_dir = os.path.join(run_dir, 'Demultiplexing')
if not os.path.exists(demux_dir):
return 'TO_START'
elif os.path.exists(os.path.join(demux_dir, 'Stats', 'DemultiplexingStats.xml')):
return 'COMPLETED'
else:
return 'IN_PROGRESS'
class TestTracker(unittest.TestCase):
""" run_tracker.py script tests
"""
@classmethod
def setUpClass(self):