Legacy code from Centrifuge

[syncrotron]

MICAS/server/app/main/utils/tasks.py

Lines 79 to 142 in 57338a1

	if bacteria or archaea or virus:
	# Construct db_string first
	db_list = []
	if bacteria:
	db_list.append('bacteria')
	if archaea:
	db_list.append('archaea')
	if virus:
	db_list.append('viral')
	db_string = ",".join([str(x) for x in db_list])
	logger.debug("DOWNLOAD_DATABASE: Downloading " + db_string + " database(s) from NCBI")
	self.update_state(
	state="PROGRESS",
	meta={
	'percent-done': 55,
	'message' : "Downloading " + db_string + " database(s) from NCBI",
	'project_id' : project_id
	}
	)
	cmd = ['centrifuge-download -o ' + app_location_database + 'library -m -d ' + db_string + ' refseq']
	logger.debug(f"CMD:\n {cmd}")
	outfile = open(app_location_database + 'seqid2taxid.map', 'a+')
	err_file = open(app_location_database + 'download_err.txt', 'w+')
	try:
	# Download the database.
	download_db_cmd_output = subprocess.Popen(
	cmd,
	shell=True,
	stdout=outfile,
	stderr=err_file
	)
	download_db_cmd_output.communicate()
	download_db_cmd_output.wait()
	except (OSError, subprocess.CalledProcessError) as exception:
	logger.error(str(exception))
	return "ER1"
	else:
	logger.debug("DOWNLOAD_DATABASE: Successfully downloaded " + db_string + " database(s) from NCBI")
	self.update_state(
	state="PROGRESS",
	meta={
	'percent-done': 90,
	'message' : "Successfully downloaded " + db_string + "database(s) from NCBI",
	'project_id' : project_id
	}
	)
	import glob
	# Putting all the query sequences in one, input_sequences file.
	logger.debug("DOWNLOAD_DATABASE: Concatenating all the sequence files.")
	self.update_state(state="PROGRESS",
	meta={'percent-done': 95, 'message': "Concatenating all the sequence files.",
	'project_id' : project_id}
	)
	with open(app_location_database + 'input_sequences.fa', 'wb') as outfile:
	for filename in glob.glob(app_location_database + 'library/*/*.fna'):
	with open(filename, 'rb') as readfile:
	shutil.copyfileobj(readfile, outfile)

The above code chunk is left over from our old use of centrifuge. This now does nothing but produce errors, and should be removed or updated.

[syncrotron]

This was resolved in the merge of "Centrifuge Cleanup"