def test_salmontools_with_bad_processor(self):
"""Test salmontools with a bad processor key."""
test_dir = '/home/user/data_store/salmontools/'
job_context = {
'job_id': 123,
'job': ProcessorJob.objects.create(),
'pipeline': Pipeline(name="Salmon"),
'input_file_path': test_dir + 'double_input/reads_1.fastq',
'input_file_path_2': test_dir + 'double_input/reads_2.fastq',
'salmontools_directory': test_dir + 'double_salmontools/',
'salmontools_archive': test_dir + 'salmontools-result.tar.gz',
'output_directory': test_dir + 'double_output/'
}
os.makedirs(job_context["salmontools_directory"], exist_ok=True)
homo_sapiens = Organism.get_object_for_name("HOMO_SAPIENS")
sample = Sample()
sample.organism = homo_sapiens
sample.save()
job_context["sample"] = sample
# Set the wrong yml filename on purpose to mess up Salmontools processor
original_yml_file = utils.ProcessorEnum['SALMONTOOLS'].value['yml_file']
utils.ProcessorEnum['SALMONTOOLS'].value['yml_file'] = 'foobar.yml'
salmon._run_salmontools(job_context)
self.assertEqual(job_context["success"], False)
self.assertTrue(job_context["job"].failure_reason.startswith('Failed to set processor:'))
# Change yml filename back
utils.ProcessorEnum['SALMONTOOLS'].value['yml_file'] = original_yml_file
def test_single_read(self):
"""Test outputs when the sample has one read only."""
job_context = {
'job_id': 456,
'job': ProcessorJob(),
'pipeline': Pipeline(name="Salmon"),
'input_file_path': self.test_dir + 'single_input/single_read.fastq',
'output_directory': self.test_dir + 'single_output/',
'salmontools_directory': self.test_dir + 'single_salmontools/',
'salmontools_archive': self.test_dir + 'salmontools-result.tar.gz',
'computed_files': []
}
os.makedirs(job_context["salmontools_directory"], exist_ok=True)
homo_sapiens = Organism.get_object_for_name("HOMO_SAPIENS")
sample = Sample()
sample.organism = homo_sapiens
sample.save()
job_context["sample"] = sample
salmon._run_salmontools(job_context)
# Confirm job status
self.assertTrue(job_context["success"])
# Unpack result for checking
os.system('gunzip ' + job_context['salmontools_directory'] + "*.gz")
# Check output file
output_file = job_context['salmontools_directory'] + 'unmapped_by_salmon.fa'
expected_output_file = self.test_dir + 'expected_single_output/unmapped_by_salmon.fa'
self.assertTrue(identical_checksum(output_file, expected_output_file))