Mercurial > repos > greg > gene_family_integrator
diff utils.py @ 14:0dd84595cf37 draft
Uploaded
author | greg |
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date | Fri, 05 May 2017 09:33:13 -0400 |
parents | 109a0eb7791f |
children | 27c0651f04e3 |
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--- a/utils.py Fri May 05 09:33:06 2017 -0400 +++ b/utils.py Fri May 05 09:33:13 2017 -0400 @@ -1,11 +1,30 @@ import os import shutil +import subprocess import sys +FSTDERR = 'stderr.txt' +FSTDOUT = 'stdout.txt' -def check_execution_errors(rc, stderr): + +def check_execution_errors(rc, fstderr, fstdout): if rc != 0: - stop_err(stderr.read()) + fh = open(fstdout, 'rb') + out_msg = fh.read() + fh.close() + fh = open(fstderr, 'rb') + err_msg = fh.read() + fh.close() + msg = '%s\n%s\n' % (str(out_msg), str(err_msg)) + stop_err(msg) + + +def get_response_buffers(): + fstderr = os.path.join(os.getcwd(), FSTDERR) + fherr = open(fstderr, 'wb') + fstdout = os.path.join(os.getcwd(), FSTDOUT) + fhout = open(fstdout, 'wb') + return fherr, fhout def move_directory_files(source_dir, destination_dir): @@ -18,9 +37,18 @@ shutil.move(source_entry, destination_directory) +def run_command(cmd): + fherr, fhout = get_response_buffers() + proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True) + rc = proc.wait() + # Check results. + fherr.close() + fhout.close() + check_execution_errors(rc, fstderr, fstdout) + + def stop_err(msg): - sys.stderr.write(msg) - sys.exit(1) + sys.exit(msg) def write_html_output(output, title, dir):