Maj terminée. Pour consulter la release notes associée voici le lien :
https://about.gitlab.com/releases/2021/07/07/critical-security-release-gitlab-14-0-4-released/

Une nouvelle version du portail de gestion des comptes externes sera mise en production lundi 09 août. Elle permettra d'allonger la validité d'un compte externe jusqu'à 3 ans. Pour plus de détails sur cette version consulter : https://doc-si.inria.fr/x/FCeS

Commit 6996ee8c authored by Marc Duez's avatar Marc Duez
Browse files

server : task.py > use sequence file name for output file

-print vidjil.fuse cmd in scheduller output before start
parent f54c08cc
# coding: utf8 # coding: utf8
import os
TASK_TIMEOUT = 2 * 3600 TASK_TIMEOUT = 2 * 3600
...@@ -76,6 +77,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse): ...@@ -76,6 +77,7 @@ def run_vidjil(id_file, id_config, id_data, id_fuse):
## filepath du fichier de séquence ## filepath du fichier de séquence
row = db(db.sequence_file.id==id_file).select() row = db(db.sequence_file.id==id_file).select()
filename = row[0].data_file filename = row[0].data_file
output_filename = os.path.splitext(row[0].data_file)[0]
seq_file = upload_folder+filename seq_file = upload_folder+filename
id_patient = row[0].patient_id id_patient = row[0].patient_id
...@@ -84,19 +86,20 @@ def run_vidjil(id_file, id_config, id_data, id_fuse): ...@@ -84,19 +86,20 @@ def run_vidjil(id_file, id_config, id_data, id_fuse):
vidjil_germline = db.config[id_config].germline vidjil_germline = db.config[id_config].germline
## commande complete ## commande complete
cmd = vidjil_path+'/vidjil ' + ' -o ' + out_folder cmd = vidjil_path+'/vidjil ' + ' -o ' + out_folder + " -b " + output_filename
if not vidjil_germline == 'multi': if not vidjil_germline == 'multi':
cmd += ' -G ' + germline_folder + vidjil_germline cmd += ' -G ' + germline_folder + vidjil_germline
cmd += ' ' + vidjil_cmd + ' '+ seq_file cmd += ' ' + vidjil_cmd + ' '+ seq_file
## execute la commande vidjil ## execute la commande vidjil
print "===Vidjil output==="
print cmd
p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True) p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
p.wait() p.wait()
print "===Vidjil output==="
print p.stdout.read() print p.stdout.read()
## récupération du fichier data.json généré ## récupération du fichier data.json généré
results_filepath = os.path.abspath(out_folder+"vidjil.data") results_filepath = os.path.abspath(out_folder+output_filename+".vidjil")
stream = open(results_filepath, 'rb') stream = open(results_filepath, 'rb')
## insertion dans la base de donnée ## insertion dans la base de donnée
...@@ -123,9 +126,11 @@ def run_vidjil(id_file, id_config, id_data, id_fuse): ...@@ -123,9 +126,11 @@ def run_vidjil(id_file, id_config, id_data, id_fuse):
cmd = "python ../fuse.py -o "+output_file+" -t 100 "+files cmd = "python ../fuse.py -o "+output_file+" -t 100 "+files
print "===fuse output==="
print cmd
p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True) p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
p.wait() p.wait()
print "===fuse output==="
print p.stdout.read() print p.stdout.read()
......
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