Merge branch 'genobioinfo' into 'master'

copy bash script on remote server to be able to execute it

See merge request !151

workflows/download_symlink/components/createsymlink.py

@@ -29,6 +29,7 @@ def create_symbolik_link (ids_dump_path, output_list, user_script, username, pas
     import pickle
     import subprocess
     import logging
+    import shlex
 
     from ng6.config_reader import NG6ConfigReader
     from ng6.utils import Utils, SSH
@@ -77,17 +78,17 @@ def create_symbolik_link (ids_dump_path, output_list, user_script, username, pas
         #    user_script = user_script.replace("/home/ng6/work/", "/oldwork/ng6/")
         #    user_script = user_script.replace("/work/ng6/", "/oldwork/ng6/")
         #    logging.getLogger("create_symbolik_link").debug("user_script = "+user_script)
-        logging.getLogger("create_symbolik_link").debug("Copy " + user_script + " to " + server+output_folder)
-        cmd = 'curl --insecure --user '+username+':'+password+' -T '+user_script+' sftp://'+server+output_folder
+        logging.getLogger("create_symbolik_link").debug("Copy " + user_script + " to " + os.path.join(server,output_folder+'/'))
+        cmd = "curl --insecure --user '"+username+":"+password+"' -T "+user_script+" sftp://"+os.path.join(server,output_folder+'/')
         args = shlex.split(cmd)
         process = subprocess.Popen(args, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         stdout, stderr = process.communicate()
         logging.getLogger("create_symbolik_link").debug("curl stdout = "+ str(stdout))
         logging.getLogger("create_symbolik_link").debug("curl stderr = "+ str(stderr))
-        logging.getLogger("create_symbolik_link").debug("Execute bash "+output_folder+os.path.basename(user_script) +" on " + server + " on behalf of " + username)
-        s.cmd('bash ' + output_folder+os.path.basename(user_script))
-        logging.getLogger("create_symbolik_link").debug("Delete "+output_folder+os.path.basename(user_script) +" on " + server + " on behalf of " + username)
-        s.cmd('rm ' + output_folder+os.path.basename(user_script))
+        logging.getLogger("create_symbolik_link").debug("Execute bash "+os.path.join(output_folder,os.path.basename(user_script)) +" on " + server + " on behalf of " + username)
+        s.cmd('bash ' + os.path.join(output_folder,os.path.basename(user_script)))
+        logging.getLogger("create_symbolik_link").debug("Delete "+os.path.join(output_folder,os.path.basename(user_script)) +" on " + server + " on behalf of " + username)
+        s.cmd('rm ' + os.path.join(output_folder,os.path.basename(user_script)))
         #s.cmd('bash %s'%user_script)
         logging.getLogger("create_symbolik_link").debug("After s.cmd(")