def check_salmon_quant(self, job_context, sample_dir):
"""Helper function that calls salmon._run_salmon and confirms
strong correlation.
"""
# Clean up if there were previous tests, but we still need that directory.
shutil.rmtree(job_context['output_directory'], ignore_errors=True)
os.makedirs(job_context["output_directory"], exist_ok=True)
job_context = salmon._determine_index_length(job_context)
job_context = salmon._find_or_download_index(job_context)
# This is a brittle/hacky patch.
# However I am unsure why the double_reads reads are
# determined to be short but require a long index to be
# processed successfully.
if "test_experiment" in sample_dir:
job_context["index_directory"] = job_context["index_directory"].replace("SHORT", "LONG")
job_context = salmon._run_salmon(job_context)
job_context = salmon.get_tximport_inputs(job_context)
job_context = salmon.tximport(job_context)
output_quant_filename = os.path.join(job_context['output_directory'], 'quant.sf')
self.assertTrue(os.path.exists(output_quant_filename))
# Confirm strong correlation between the new "quant.sf" and reference file
ref_quant_filename = os.path.join(sample_dir, 'ref_files/quant.sf')
self.assertTrue(strong_quant_correlation(ref_quant_filename, output_quant_filename))
def test_salmon_determine_index_length_double_read(self):
"""Test that the right length is calculated when the sample has two reads."""
job, files = prepare_job()
job_context = salmon._set_job_prefix({'original_files': files,
'job_id': job})
job_context = salmon._prepare_files(job_context)
results = salmon._determine_index_length(job_context)
self.assertEqual(results['index_length_raw'], 41)
self.assertEqual(results['index_length'], 'short')
def test_success(self):
"""Tests the successful path of the module under test."""
logger.info("STARTING SALMON SUCCESS TEST!!!!!!!!")
# Set up test environment.
batch, first_file, second_file = init_objects()
_insert_salmon_index()
# Change the batch/files to point to test-specific locations
batch.platform_accession_code = "TEST"
batch.save()
first_file.internal_location = "TEST/SALMON"
first_file.save()
second_file.internal_location = "TEST/SALMON"
second_file.save()
processor_job = ProcessorJob.create_job_and_relationships(
batches=[batch])
processor_job.save()
job_context = utils.start_job({
"job": processor_job,
"job_id": processor_job.id
})
job_context = salmon._set_job_prefix(job_context)
# Ensure temp dir isn't leftover from a previous test.
temp_dir = first_file.get_temp_dir(job_context["job_dir_prefix"])
shutil.rmtree(temp_dir, ignore_errors=True)
# One of the functions being tested:
job_context = salmon._prepare_files(job_context)
input_file_path = job_context["input_file_path"]
self.assertIsInstance(input_file_path, str)
self.assertTrue(os.path.isfile(input_file_path))
input_file_path_2 = job_context["input_file_path_2"]
self.assertIsInstance(input_file_path_2, str)
self.assertTrue(os.path.isfile(input_file_path_2))
output_directory_path = job_context["output_directory"]
self.assertIsInstance(output_directory_path, str)
self.assertTrue(os.path.isdir(output_directory_path))
job_context = salmon._determine_index_length(job_context)
# The 'kmer_size' key has been added to job_context with the
# correct value.
self.assertEqual(job_context["kmer_size"], "23")
# Another function being tested
job_context = salmon._download_index(job_context)
self.assertTrue(job_context["success"])
self.assertTrue("index_directory" in job_context)
self.assertTrue(os.path.isdir(job_context["index_directory"]))
self.assertEqual(9, len(os.listdir(job_context["index_directory"])))
# Another function being tested
job_context = salmon._run_salmon(job_context)
self.assertTrue(job_context["success"])
self.assertGreater(len(os.listdir(output_directory_path)), 1)
# The last function to test
job_context = salmon._zip_and_upload(job_context)
self.assertTrue(job_context["success"])
self.assertTrue(os.path.exists(first_file.get_processed_path()))
# Clean up both input and output files
first_file.remove_temp_directory()
shutil.rmtree(first_file.get_processed_dir())
logger.info("ENDING SALMON SUCCESS TEST!!!!!!!!")