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#!/usr/bin/python3
############################################################################
# Copyright (c) 2015-2017 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
#script for testing SPAdes
#provide a path to .info file
import sys
import os
import shutil
import getopt
import re
import datetime
import argparse
import subprocess
from traceback import print_exc
sys.path.append('./src/spades_pipeline/')
import process_cfg
sys.path.append('./src/test/teamcity/')
import teamcity_support
from teamcity_support import *
### main ###
try:
if len(sys.argv) == 1:
command = 'python3 {} -h'.format(sys.argv[0])
subprocess.call(command, shell=True)
sys.exit(1)
sys.stderr = sys.stdout
exit_code = 0
args = parse_args()
dataset_info = load_info(args.info)
working_dir = os.getcwd()
output_dir = create_output_dir(args, dataset_info)
save_run_info(args, output_dir)
#compile
ecode = compile_spades(args, dataset_info, working_dir)
if ecode != 0:
log.err("Compilation finished abnormally with exit code " + str(ecode))
sys.exit(3)
#run spades
spades_dir = working_dir
if args.spades_path:
spades_dir = args.spades_path
log.log("Different spades.py path specified: " + spades_dir)
spades_cmd = make_spades_cmd(args, dataset_info, spades_dir, output_dir)
#log.log("Launching: " + spades_cmd)
ecode = os.system(spades_cmd)
if ecode != 0:
log.err("SPAdes finished abnormally with exit code " + str(ecode))
sys.exit(4)
#reads quality
if 'reads_quality_params' in dataset_info.__dict__:
exit_code = run_reads_assessment(dataset_info, working_dir, output_dir)
#QUAST
rewrite_latest = True
contigs = get_contigs_list(args, dataset_info)
if 'quast_params' in dataset_info.__dict__:
ecode = quast_analysis(contigs, dataset_info, output_dir)
if ecode != 0:
rewrite_latest = False
log.err("QUAST analysis did not pass, exit code " + str(ecode))
exit_code = ecode
#etalon saves
if 'etalon_saves' in dataset_info.__dict__:
log.log("Comparing etalon saves now")
ecode = os.system(os.path.join(spades_dir, "./src/test/teamcity/detect_diffs.sh") + " " + output_dir + " " + dataset_info.etalon_saves)
if ecode != 0:
rewrite_latest = False
log.err("Comparing etalon saves did not pass, exit code " + str(ecode))
exit_code = 12
#compare misassemblies
contig_storage_dir = get_contigs_storage_dir(args, dataset_info)
ecode, rewrite = compare_misassemblies(contigs, dataset_info, contig_storage_dir, output_dir)
rewrite_latest = rewrite_latest and rewrite
if ecode != 0:
log.err('Failed to compare misassemblies')
#save contigs to storage
contigs = get_contigs_list(args, dataset_info, True)
save_contigs(args, output_dir, contig_storage_dir, contigs, rewrite_latest)
#save quast report as build artifact
artifact_dir = os.path.join(working_dir, "quast_reports")
save_quast_report(contigs, dataset_info, contig_storage_dir, output_dir, artifact_dir)
sys.exit(exit_code)
except SystemExit:
raise
except:
log.err("The following unexpected error occured during the run:")
print_exc()
sys.exit(239)
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