def test_clone_analysis_dir_copy_fastqs(self):
"""
clone: copies an analysis directory
"""
# Make a source analysis dir
analysis_dir = MockAnalysisDirFactory.bcl2fastq2(
"190116_M01234_0002_AXYZ123",
platform="miseq",
paired_end=True,
no_lane_splitting=False,
include_stats_files=True,
top_dir=self.dirn)
analysis_dir.create()
ap = AutoProcess(analysis_dir.dirn)
UpdateAnalysisDir(ap).add_processing_report()
ap.add_directory("primary_data/190116_M01234_0002_AXYZ123")
# Make a copy
clone_dir = os.path.join(self.dirn, "190116_M01234_0002_AXYZ123_copy")
self.assertFalse(os.path.exists(clone_dir))
clone(ap, clone_dir, copy_fastqs=True)
self.assertTrue(os.path.isdir(clone_dir))
# Check contents
for subdir in ('logs', 'ScriptCode'):
d = os.path.join(clone_dir, subdir)
self.assertTrue(os.path.isdir(d), "Missing '%s'" % subdir)
for filen in (
'SampleSheet.orig.csv',
'custom_SampleSheet.csv',
'auto_process.info',
'metadata.info',
'statistics.info',
'statistics_full.info',
'per_lane_statistics.info',
'per_lane_sample_stats.info',
'processing_qc.html',
):
f = os.path.join(clone_dir, filen)
self.assertTrue(os.path.isfile(f), "Missing '%s'" % filen)
# Check unaligned
unaligned = os.path.join(clone_dir, 'bcl2fastq')
self.assertTrue(os.path.isdir(unaligned))
# Check primary data
primary_data = os.path.join(clone_dir, 'primary_data',
'190116_M01234_0002_AXYZ123')
self.assertTrue(os.path.islink(primary_data))
# Check projects
for proj in ('AB', 'CDE', 'undetermined'):
d = os.path.join(clone_dir, proj)
self.assertTrue(os.path.isdir(d), "Missing '%s'" % proj)
# Check parameters
params = AnalysisDirParameters(
filen=os.path.join(clone_dir, 'auto_process.info'))
self.assertEqual(params.sample_sheet,
os.path.join(clone_dir, "custom_SampleSheet.csv"))
self.assertEqual(params.primary_data_dir,
os.path.join(clone_dir, "primary_data"))
def test_clone_fails_if_target_dir_exists(self):
"""
clone: raises an exception if target dir already exists
"""
# Make a source analysis dir
analysis_dir = MockAnalysisDirFactory.bcl2fastq2(
"190116_M01234_0002_AXYZ123",
platform="miseq",
paired_end=True,
no_lane_splitting=False,
include_stats_files=True,
top_dir=self.dirn)
analysis_dir.create()
ap = AutoProcess(analysis_dir.dirn)
UpdateAnalysisDir(ap).add_processing_report()
ap.add_directory("primary_data/190116_M01234_0002_AXYZ123")
# Make target dir
clone_dir = os.path.join(self.dirn, "190116_M01234_0002_AXYZ123_copy")
os.mkdir(clone_dir)
# Try to copy source dir
self.assertRaises(Exception, clone, ap, clone_dir)
def test_clone_analysis_dir_empty_params(self):
"""
clone: copies an analysis directory when parameter file is empty
"""
# Make a source analysis dir
analysis_dir = MockAnalysisDirFactory.bcl2fastq2(
"190116_M01234_0002_AXYZ123",
platform="miseq",
paired_end=True,
no_lane_splitting=False,
include_stats_files=True,
top_dir=self.dirn)
analysis_dir.create()
ap = AutoProcess(analysis_dir.dirn)
UpdateAnalysisDir(ap).add_processing_report()
ap.add_directory("primary_data/190116_M01234_0002_AXYZ123")
# Remove data from parameter file
parameter_file = ap.parameter_file
tmp_parameter_file = os.path.join(self.dirn, 'new_params.tmp')
del (ap)
with open(parameter_file, 'r') as fp:
with open(tmp_parameter_file, 'w') as fpp:
for line in fp:
line = "%s\t." % line.split('\t')[0]
fpp.write(line)
os.remove(parameter_file)
os.rename(tmp_parameter_file, parameter_file)
ap = AutoProcess(analysis_dir.dirn)
# Make a copy
clone_dir = os.path.join(self.dirn, "190116_M01234_0002_AXYZ123_copy")
self.assertFalse(os.path.exists(clone_dir))
clone(ap, clone_dir, exclude_projects=False)
self.assertTrue(os.path.isdir(clone_dir))
# Check contents
for subdir in ('logs', 'ScriptCode'):
d = os.path.join(clone_dir, subdir)
self.assertTrue(os.path.isdir(d), "Missing '%s'" % subdir)
for filen in (
'SampleSheet.orig.csv',
'custom_SampleSheet.csv',
'auto_process.info',
'metadata.info',
'statistics.info',
'statistics_full.info',
'per_lane_statistics.info',
'per_lane_sample_stats.info',
'processing_qc.html',
):
f = os.path.join(clone_dir, filen)
self.assertTrue(os.path.isfile(f), "Missing '%s'" % filen)
# Check unaligned
unaligned = os.path.join(clone_dir, 'bcl2fastq')
self.assertTrue(os.path.islink(unaligned))
# Check primary data
primary_data = os.path.join(clone_dir, 'primary_data',
'190116_M01234_0002_AXYZ123')
self.assertFalse(os.path.exists(primary_data))
# Check projects
for proj in ('AB', 'CDE', 'undetermined'):
d = os.path.join(clone_dir, proj)
self.assertTrue(os.path.exists(d), "Missing '%s'" % proj)
