epicov: File transfer failing in batch.py script

[GopiGugan]

[covizu@Paphlagon ~]$ tail batch.log 
R[write to console]:  library ‘/usr/share/R/library’ contains no packages

ssh: connect to host filogeneti.ca port 22: Connection timed out
scp: Connection closed
Traceback (most recent call last):
  File "/home/covizu/covizu/batch.py", line 214, in <module>
    subprocess.check_call(['scp', nwk_file, '{}/timetree.nwk'.format(server_epicov)])
  File "/usr/lib64/python3.11/subprocess.py", line 413, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['scp', 'data/timetree.2023-10-21T06:22:09.nwk', 'filogeneti.ca:/var/www/html/epicov/data/timetree.nwk']' returned non-zero exit status 255.

[GopiGugan]

[covizu@Paphlagon covizu]$ python3
Python 3.11.3 (main, Apr  5 2023, 00:00:00) [GCC 12.2.1 20221121 (Red Hat 12.2.1-4)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import subprocess
>>> subprocess.check_call(['scp', 'data/timetree.2023-10-21T06:22:09.nwk', 'filogeneti.ca:/var/www/html/epicov/data/timetree_test.nwk'])
timetree.2023-10-21T06:22:09.nwk                                                                                                                                                           100%   69KB  29.5MB/s   00:00    
0

[GopiGugan]

There is a rule in place on the webserver to prevent SSH brute force attacks.

As a result, we are running into the SSH timeout when running multiple scp commands sequentially: https://github.com/PoonLab/covizu/blob/4ab1ba45b919a45d974c0dc58bf64f09c7dfadb1/batch.py#L208-L215

[ArtPoon]

Let's add time.sleep(5) commands between calls to scp in the local copy of batch.py temporarily until we switch from the VM webserver back to ccr5.

[ArtPoon]

Moved back to original webserver, this isn't an issue anymore