def test_get_sample_pipeline_log(self):
"""Get the sample pipeline logfile
"""
sample = td.generate_sample()
# Assert that an empty directory returns None
self.assertIsNone(
sq.get_sample_pipeline_log(self.rootdir, sample),
"Getting a sample log from an empty directory did not return None")
# Assert that non-relevant log files are not returned
for n in range(5):
utils.touch_file(
os.path.join(self.rootdir,
"{}-bcbb.log".format(td.generate_sample())))
self.assertIsNone(
sq.get_sample_pipeline_log(self.rootdir, sample),
"Getting a non-existing sample log did not return None")
# Assert that the correct log file is returned when it exists
utils.touch_file(
os.path.join(self.rootdir, "{}-bcbb.log".format(sample)))
self.assertEqual(
os.path.join(self.rootdir, "{}-bcbb.log".format(sample)),
sq.get_sample_pipeline_log(self.rootdir, sample),
"Getting an existing sample log file did not return the expected file"
)
def test_fastq_screen_finished(self):
"""Detecting finished state of fastq_screen
"""
# Assert that an empty directory doesn't indicate finished state
self.assertFalse(sq.fastq_screen_finished(self.rootdir),
"Fastq screen should not be considered finished without output files")
# Create an output file and corresponding png but no rows in output
sample_file = os.path.join(self.rootdir,"{}_fastq_screen.txt".format(td.generate_sample()))
png_file = "{}.png".format(os.path.splitext(sample_file)[0])
utils.touch_file(sample_file)
utils.touch_file(png_file)
self.assertFalse(sq.fastq_screen_finished(self.rootdir),
"Fastq screen should not be considered finished with empty output file")
# Write some output and assert fastq_screen is detected as finished
with open(sample_file,"w") as fh:
for n in range(5):
fh.write("{}\n".format(str(n)))
self.assertTrue(sq.fastq_screen_finished(self.rootdir),
"Fastq screen should be considered finished with non-empty output file and corresponding png")
# Remove the png and assert fastq_screen is not finished
os.unlink(png_file)
self.assertFalse(sq.fastq_screen_finished(self.rootdir),
"Fastq screen should not be considered finished with non-empty output file but without corresponding png")
def test_fastq_screen_finished(self):
"""Detecting finished state of fastq_screen
"""
# Assert that an empty directory doesn't indicate finished state
self.assertFalse(sq.fastq_screen_finished(self.rootdir),
"Fastq screen should not be considered finished without output files")
# Create an output file and corresponding png but no rows in output
sample_file = os.path.join(self.rootdir,"{}_fastq_screen.txt".format(td.generate_sample()))
png_file = "{}.png".format(os.path.splitext(sample_file)[0])
utils.touch_file(sample_file)
utils.touch_file(png_file)
self.assertFalse(sq.fastq_screen_finished(self.rootdir),
"Fastq screen should not be considered finished with empty output file")
# Write some output and assert fastq_screen is detected as finished
with open(sample_file,"w") as fh:
for n in range(5):
fh.write("{}\n".format(str(n)))
self.assertTrue(sq.fastq_screen_finished(self.rootdir),
"Fastq screen should be considered finished with non-empty output file and corresponding png")
# Remove the png and assert fastq_screen is not finished
os.unlink(png_file)
self.assertFalse(sq.fastq_screen_finished(self.rootdir),
"Fastq screen should not be considered finished with non-empty output file but without corresponding png")
def test_get_sample_pipeline_log(self):
"""Get the sample pipeline logfile
"""
sample = td.generate_sample()
# Assert that an empty directory returns None
self.assertIsNone(sq.get_sample_pipeline_log(self.rootdir,sample),
"Getting a sample log from an empty directory did not return None")
# Assert that non-relevant log files are not returned
for n in range(5):
utils.touch_file(os.path.join(self.rootdir,"{}-bcbb.log".format(td.generate_sample())))
self.assertIsNone(sq.get_sample_pipeline_log(self.rootdir,sample),
"Getting a non-existing sample log did not return None")
# Assert that the correct log file is returned when it exists
utils.touch_file(os.path.join(self.rootdir,"{}-bcbb.log".format(sample)))
self.assertEqual(os.path.join(self.rootdir,"{}-bcbb.log".format(sample)),sq.get_sample_pipeline_log(self.rootdir,sample),
"Getting an existing sample log file did not return the expected file")
