def setUpClass(self):
""" Creates the following directory tree for testing purposes:
tmp/
|__ 141124_ST-COMPLETED_01_AFCIDXX
| |__ RunInfo.xml
| |__ Demultiplexing
| | |__ Stats
| | |__ DemultiplexingStats.xml
| |__ RTAComplete.txt
|__ 141124_ST-INPROGRESS_02_AFCIDXX
| |__ RunInfo.xml
| |__ Demultiplexing
| |__ RTAComplete.txt
|__ 141124_ST-RUNNING_03_AFCIDXX
| |__ RunInfo.xml
|__ 141124_ST-TOSTART_04_FCIDXXX
|__ RunInfo.xml
|__ RTAComplete.txt
"""
self.tmp_dir = os.path.join(tempfile.mkdtemp(), 'tmp')
self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')
running = os.path.join(self.tmp_dir, '141124_ST-RUNNING1_03_AFCIDXX')
to_start = os.path.join(self.tmp_dir, '141124_ST-TOSTART1_04_FCIDXXX')
in_progress = os.path.join(self.tmp_dir, '141124_ST-INPROGRESS1_02_AFCIDXX')
completed = os.path.join(self.tmp_dir, '141124_ST-COMPLETED1_01_AFCIDXX')
finished_runs = [to_start, in_progress, completed]
# Create runs directory structure
os.makedirs(self.tmp_dir)
os.makedirs(running)
os.makedirs(to_start)
os.makedirs(os.path.join(in_progress, 'Demultiplexing'))
os.makedirs(os.path.join(completed, 'Demultiplexing', 'Stats'))
# Create files indicating that the run is finished
for run in finished_runs:
open(os.path.join(run, 'RTAComplete.txt'), 'w').close()
# Create files indicating that the preprocessing is done
open(os.path.join(completed, 'Demultiplexing', 'Stats', 'DemultiplexingStats.xml'), 'w').close()
# Create transfer file and add the completed run
with open(self.transfer_file, 'w') as f:
tsv_writer = csv.writer(f, delimiter='\t')
tsv_writer.writerow([os.path.basename(completed), str(datetime.now())])
# Move sample RunInfo.xml file to every run directory
for run in [running, to_start, in_progress, completed]:
shutil.copy('data/RunInfo.xml', run)
shutil.copy('data/runParameters.xml', run)
# Create run objects
# Jose : add tests for other sequencers
self.running = HiSeqX_Run(os.path.join(self.tmp_dir,
'141124_ST-RUNNING1_03_AFCIDXX'),
CONFIG["analysis"]["HiSeqX"])
self.to_start = Run(os.path.join(self.tmp_dir,
'141124_ST-TOSTART1_04_FCIDXXX'),
CONFIG["analysis"]["HiSeqX"])
self.in_progress = Run(os.path.join(self.tmp_dir,
'141124_ST-INPROGRESS1_02_AFCIDXX'),
CONFIG["analysis"]["HiSeqX"])
self.completed = Run(os.path.join(self.tmp_dir,
'141124_ST-COMPLETED1_01_AFCIDXX'),
CONFIG["analysis"]["HiSeqX"])
self.finished_runs = [self.to_start, self.in_progress, self.completed]
self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')
class TestTracker(unittest.TestCase):
""" analysis.py script tests
"""
@classmethod
def setUpClass(self):
""" Creates the following directory tree for testing purposes:
tmp/
|__ 141124_ST-COMPLETED_01_AFCIDXX
| |__ RunInfo.xml
| |__ Demultiplexing
| | |__ Stats
| | |__ DemultiplexingStats.xml
| |__ RTAComplete.txt
|__ 141124_ST-INPROGRESS_02_AFCIDXX
| |__ RunInfo.xml
| |__ Demultiplexing
| |__ RTAComplete.txt
|__ 141124_ST-RUNNING_03_AFCIDXX
| |__ RunInfo.xml
|__ 141124_ST-TOSTART_04_FCIDXXX
|__ RunInfo.xml
|__ RTAComplete.txt
"""
self.tmp_dir = os.path.join(tempfile.mkdtemp(), 'tmp')
self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')
running = os.path.join(self.tmp_dir, '141124_ST-RUNNING1_03_AFCIDXX')
to_start = os.path.join(self.tmp_dir, '141124_ST-TOSTART1_04_FCIDXXX')
in_progress = os.path.join(self.tmp_dir, '141124_ST-INPROGRESS1_02_AFCIDXX')
completed = os.path.join(self.tmp_dir, '141124_ST-COMPLETED1_01_AFCIDXX')
finished_runs = [to_start, in_progress, completed]
# Create runs directory structure
os.makedirs(self.tmp_dir)
os.makedirs(running)
os.makedirs(to_start)
os.makedirs(os.path.join(in_progress, 'Demultiplexing'))
os.makedirs(os.path.join(completed, 'Demultiplexing', 'Stats'))
# Create files indicating that the run is finished
for run in finished_runs:
open(os.path.join(run, 'RTAComplete.txt'), 'w').close()
# Create files indicating that the preprocessing is done
open(os.path.join(completed, 'Demultiplexing', 'Stats', 'DemultiplexingStats.xml'), 'w').close()
# Create transfer file and add the completed run
with open(self.transfer_file, 'w') as f:
tsv_writer = csv.writer(f, delimiter='\t')
tsv_writer.writerow([os.path.basename(completed), str(datetime.now())])
# Move sample RunInfo.xml file to every run directory
for run in [running, to_start, in_progress, completed]:
shutil.copy('data/RunInfo.xml', run)
shutil.copy('data/runParameters.xml', run)
# Create run objects
# Jose : add tests for other sequencers
self.running = HiSeqX_Run(os.path.join(self.tmp_dir,
'141124_ST-RUNNING1_03_AFCIDXX'),
CONFIG["analysis"]["HiSeqX"])
self.to_start = Run(os.path.join(self.tmp_dir,
'141124_ST-TOSTART1_04_FCIDXXX'),
CONFIG["analysis"]["HiSeqX"])
self.in_progress = Run(os.path.join(self.tmp_dir,
'141124_ST-INPROGRESS1_02_AFCIDXX'),
CONFIG["analysis"]["HiSeqX"])
self.completed = Run(os.path.join(self.tmp_dir,
'141124_ST-COMPLETED1_01_AFCIDXX'),
CONFIG["analysis"]["HiSeqX"])
self.finished_runs = [self.to_start, self.in_progress, self.completed]
self.transfer_file = os.path.join(self.tmp_dir, 'transfer.tsv')
@classmethod
def tearDownClass(self):
shutil.rmtree(self.tmp_dir)
def test_1_is_finished(self):
""" Is finished should be True only if "RTAComplete.txt" file is present...
"""
self.assertFalse(self.running._is_sequencing_done())
self.assertTrue(all(map(lambda run: run._is_sequencing_done, self.finished_runs)))
def test_2_processing_status(self):
""" Status of the processing depends on the generated files
"""
self.assertEqual('SEQUENCING', self.running.get_run_status())
self.assertEqual('TO_START', self.to_start.get_run_status())
self.assertEqual('IN_PROGRESS', self.in_progress.get_run_status())
self.assertEqual('COMPLETED', self.completed.get_run_status())
def test_3_is_transferred(self):
""" is_transferred should rely on the info in transfer.tsv
"""
self.assertTrue(self.completed.is_transferred(self.transfer_file))
self.assertFalse(self.running.is_transferred(self.transfer_file))
self.assertFalse(self.to_start.is_transferred(self.transfer_file))
self.assertFalse(self.in_progress.is_transferred( self.transfer_file))