def basic_process_run_results_f(f):
""" Copy each list of infiles to each outfile and delete infiles
f: file containing one set of mapping instructions per line
example f:
f1.txt f2.txt f3.txt f_combined.txt
f1.log f2.log f3.log f_combined.log
If f contained the two lines above, this function would
concatenate f1.txt, f2.txt, and f3.txt into f_combined.txt
and f1.log, f2.log, and f3.log into f_combined.log
"""
infiles_lists, out_filepaths = parse_tmp_to_final_filepath_map_file(f)
for infiles_list, out_filepath in zip(infiles_lists, out_filepaths):
try:
of = open(out_filepath, 'w')
except IOError:
raise IOError(
"Poller can't open final output file: %s" % out_filepath +
"\nLeaving individual jobs output.\n Do you have write access?"
)
for fp in infiles_list:
for line in open(fp):
of.write('%s\n' % line.strip('\n'))
of.close()
# It is a good idea to have your clean_up_callback return True.
# That way, if you get mixed up and pass it as check_run_complete_callback,
# you'll get an error right away rather than going into an infinite loop
return True
def verbose_process_run_results_f(f):
""" Copy each list of infiles to each outfile and delete infiles (verbose)
f: file containing one set of mapping instructions per line
example f:
f1.txt f2.txt f3.txt f_combined.txt
f1.log f2.log f3.log f_combined.log
If f contained the two lines above, this function would
concatenate f1.txt, f2.txt, and f3.txt into f_combined.txt
and f1.log, f2.log, and f3.log into f_combined.log
"""
infiles_lists, out_filepaths = parse_tmp_to_final_filepath_map_file(f)
for infiles_list, out_filepath in zip(infiles_lists, out_filepaths):
try:
of = open(out_filepath, 'w')
print 'Final result file (%s) contains temp files:'\
% out_filepath
except IOError:
raise IOError("Poller can't open final output file: %s" % out_filepath +
"\nLeaving individual jobs output.\n Do you have write access?")
for fp in infiles_list:
print '\t%s' % fp
for line in open(fp):
of.write(line)
of.close()
return True
def basic_process_run_results_f(f):
""" Copy each list of infiles to each outfile and delete infiles
f: file containing one set of mapping instructions per line
example f:
f1.txt f2.txt f3.txt f_combined.txt
f1.log f2.log f3.log f_combined.log
If f contained the two lines above, this function would
concatenate f1.txt, f2.txt, and f3.txt into f_combined.txt
and f1.log, f2.log, and f3.log into f_combined.log
"""
infiles_lists, out_filepaths = parse_tmp_to_final_filepath_map_file(f)
for infiles_list, out_filepath in zip(infiles_lists, out_filepaths):
try:
of = open(out_filepath, 'w')
except IOError:
raise IOError("Poller can't open final output file: %s" % out_filepath +
"\nLeaving individual jobs output.\n Do you have write access?")
for fp in infiles_list:
for line in open(fp):
of.write('%s\n' % line.strip('\n'))
of.close()
# It is a good idea to have your clean_up_callback return True.
# That way, if you get mixed up and pass it as check_run_complete_callback,
# you'll get an error right away rather than going into an infinite loop
return True
def verbose_process_run_results_f(f):
""" Copy each list of infiles to each outfile and delete infiles (verbose)
f: file containing one set of mapping instructions per line
example f:
f1.txt f2.txt f3.txt f_combined.txt
f1.log f2.log f3.log f_combined.log
If f contained the two lines above, this function would
concatenate f1.txt, f2.txt, and f3.txt into f_combined.txt
and f1.log, f2.log, and f3.log into f_combined.log
"""
infiles_lists,out_filepaths = parse_tmp_to_final_filepath_map_file(f)
for infiles_list, out_filepath in zip(infiles_lists,out_filepaths):
try:
of = open(out_filepath,'w')
print 'Final result file (%s) contains temp files:'\
% out_filepath
except IOError:
raise IOError,\
"Poller can't open final output file: %s" % out_filepath +\
"\nLeaving individual jobs output.\n Do you have write access?"
for fp in infiles_list:
print '\t%s' % fp
for line in open(fp):
of.write(line)
of.close()
return True
