def test_transcriptome(self):
self.assertEqual(Processor.objects.count(), 0) # No processor yet
proc_key = "TX_INDEX"
tx_processor = utils.find_processor(proc_key)
self.assertEqual(Processor.objects.count(), 1) # New processor created
# Validate some information of the new processor
self.assertEqual(tx_processor.name,
ProcessorEnum[proc_key].value["name"])
cmd_str = "salmon --version"
cmd_output = utils.get_cmd_lines([cmd_str])[cmd_str]
self.assertEqual(tx_processor.environment["cmd_line"][cmd_str],
cmd_output)
cmd_str = "rsem-calculate-expression --version"
cmd_output = utils.get_cmd_lines([cmd_str])[cmd_str]
self.assertEqual(tx_processor.environment["cmd_line"][cmd_str],
cmd_output)
def test_salmontools(self):
self.assertEqual(Processor.objects.count(), 0) # No processor yet
proc_key = "SALMONTOOLS"
st_processor = utils.find_processor(proc_key)
self.assertEqual(Processor.objects.count(), 1) # New processor created
# Validate some information of the new processor
self.assertEqual(st_processor.name,
utils.ProcessorEnum[proc_key].value['name'])
cmd_str = "salmontools --version"
cmd_output = utils.get_cmd_lines([cmd_str])[cmd_str]
self.assertEqual(st_processor.environment['cmd_line'][cmd_str],
cmd_output)
def test_multiqc(self):
self.assertEqual(Processor.objects.count(), 0) # No processor yet
proc_key = "MULTIQC"
multiqc_processor = utils.find_processor(proc_key)
self.assertEqual(Processor.objects.count(), 1) # New processor created
# Validate some information of the new processor
self.assertEqual(multiqc_processor.name,
utils.ProcessorEnum[proc_key].value['name'])
cmd_str = "/home/user/FastQC/fastqc --version"
cmd_output = utils.get_cmd_lines([cmd_str])[cmd_str]
self.assertEqual(multiqc_processor.environment['cmd_line'][cmd_str],
cmd_output)