Commit 1dd16482 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files pre-process stdout/scheduler_run.run_output, clean and add pre-process log

The end user should have access to the pre-process log.
parent 9153523d
......@@ -147,7 +147,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse, grep_reads,
## re schedule if pre_process is still pending
if db.sequence_file[id_file].pre_process_flag != True :
print "re-schedule"
print "Pre-process is still pending, re-schedule"
args = [id_file, id_config, id_data, id_fuse, grep_reads]
task = scheduler.queue_task("vidjil", args,
......@@ -647,22 +647,20 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
output_file = out_folder+'/'+output_filename+'.fastq'
print sequence_file_id
print pre_process_id
sequence_file = db.sequence_file[sequence_file_id]
pre_process = db.pre_process[pre_process_id]
print sequence_file
print pre_process
cmd = pre_process.command.replace( "&file1&", defs.DIR_SEQUENCES + sequence_file.data_file)
if sequence_file.data_file2:
cmd = cmd.replace( "&file2&", defs.DIR_SEQUENCES + sequence_file.data_file2)
cmd = cmd.replace( "&result&", output_file)
print "=== Pre-process %s ===" % pre_process_id
print cmd
print "==============="
log_file = open(out_folder+'/'+output_filename+'.pre.log', 'w')
......@@ -687,6 +685,10 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
pre_process_flag = True)
# Dump log in scheduler_run.run_output
for l in open(log_file):
print l,
if clean_after:
clean_cmd = "rm -rf " + out_folder
p = Popen(clean_cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
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