Question: Uploading data files to Webin upload area under Linux
1
gravatar for Michael Gruenstaeudl
19 months ago by
Berlin, Germany
Michael Gruenstaeudl40 wrote:

The European Nucleotide Archive (ENA) requires certain datasets to be uploaded to the Webin upload area (webin.ebi.ac.uk) before they can be submitted via XML files that reference the uploaded file.

According to this doc, one can use lftp to upload a data file. However, when I try to do this in practice, I find that several modifications have to be made to get anywhere near a login to the Webin upload area:

Attempting a log-in under the default settings causes a freeze at line

`ls' at 0 [FEAT negotiation...]

michael_science ~ $ lftp webin.ebi.ac.uk
lftp webin.ebi.ac.uk:~> login myWebinAccount
Password:
lftp myWebinAccount@webin.ebi.ac.uk:~> ls
`ls' at 0 [Connecting...]
`ls' at 0 [FEAT negotiation...]

Attempting a log-in upon disabling FEAT negotiation and SSL encryption goes further, but still doesn't get the job done, as it freezes at line

`ls' at 0 [Logging in...]

lftp -e 'set ftp:use-feat false; set ftp:ssl-allow false' webin.ebi.ac.uk
lftp webin.ebi.ac.uk:~> login myWebinAccount
Password:
lftp myWebinAccount@webin.ebi.ac.uk:~> ls
`ls' at 0 [Connecting...]
`ls' at 0 [Logging in...]

Has anyone successfully logged onto to the Webin upload area (webin.ebi.ac.uk) recently? If so, how?

Edit 1: Upon communication with the ENA helpdesk, it turned out to be a server problem by ENA, which seems to have been resolved for now.

sequencing sequence • 1.3k views
ADD COMMENTlink modified 19 months ago by Juke-342.8k • written 19 months ago by Michael Gruenstaeudl40

This sounds like a good case to create a direct help desk ticket with EBI.

ADD REPLYlink written 19 months ago by genomax73k
3
gravatar for SMK
19 months ago by
SMK1.9k
SMK1.9k wrote:

I was able to connect to webin.ebi.ac.uk yesterday, using both ftp webin.ebi.ac.uk command or Transmit (FTP client for OSX), but the connection was not very stable. Today I found it not possible to reach it using the same methods.

ADD COMMENTlink modified 19 months ago • written 19 months ago by SMK1.9k

@AllenKao Would you mind sharing the precise commands that you are using when ftp'ing to webin.ebi.ac.uk?

ADD REPLYlink written 19 months ago by Michael Gruenstaeudl40

Yes, in addition to the FTP client, this worked on Monday (source):

  1. Open a terminal and type ftp webin.ebi.ac.uk.
  2. Enter the username and password associated with your Webin submission account.
  3. Type bin to use binary mode.
  4. Type ls command to check the content of your drop box.
  5. Type prompt to switch off confirmation for each file uploaded.
  6. Use mput command to upload files.
  7. Use bye command to exit the ftp client.

Just tried it and now works for me:

$ ftp webin.ebi.ac.uk
Connected to webin.ebi.ac.uk (193.62.192.11).
220 (vsFTPd 2.2.2)
Name webin.ebi.ac.uk:XXXXX): myWebinAccount
331 Please specify the password.
Password:
230 Login successful.
Remote system type is UNIX.
Using binary mode to transfer files.
ADD REPLYlink modified 19 months ago • written 19 months ago by SMK1.9k

@AllenKao Thanks. I used pretty much the same commands in the past. However, I am still unable to even connect to the server, as it hangs at login:

$ ftp webin.ebi.ac.uk
Connected to hh-webin.ebi.ac.uk.
# Hangs here forever.
ADD REPLYlink written 19 months ago by Michael Gruenstaeudl40

You might contact the ENA Helpdesk: datasubs@ebi.ac.uk .

ADD REPLYlink modified 19 months ago • written 19 months ago by SMK1.9k

Michael Gruenstaeudl : This could a problem with your local firewall/security setup. I just tried ftp webin.ebi.ac.uk and was immediately presented with a login prompt.

ADD REPLYlink written 19 months ago by genomax73k

Just received an email by ENA that it was a server problem on their side. Seems to be corrected now.

ADD REPLYlink written 19 months ago by Michael Gruenstaeudl40

Interestingly, I am able to connect when I ftp directly to the IP address:

ftp 193.62.192.11
Connected to 193.62.192.11.
220 (vsFTPd 2.2.2)
Name (193.62.192.11:XXXX):
ADD REPLYlink written 19 months ago by Michael Gruenstaeudl40

It is the third day I try without success... ftp 193.62.192.11 and ftp webin.ebi.ac.uk the same...

421 Service not available, remote server has closed connection

:(

ADD REPLYlink written 19 months ago by Juke-342.8k

This must be a local issue. I just tried ftp webin.ebi.ac.uk (or 193.62.192.11) and was immediately presented with a login prompt.

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax73k

Interesting... I have tried from two different location in Sweden without success....

both are in universities.... maybe a new firewall protection ...

Ok, I have tried using a vpn and now it is working !!

ADD REPLYlink modified 19 months ago • written 19 months ago by Juke-342.8k

@Juke-34 and @genomax Actually, the issue is an unstable server on the side of ENA. It goes offline intermittently throughout the day. I was unsuccessful ftp'ing to 193.62.192.11 prior to 11:00 CEST, then successful, and since about 14:00 CEST unsuccessful again. AllenKao, in his post above, has correctly diagnosed the phenomenon.

ADD REPLYlink written 19 months ago by Michael Gruenstaeudl40
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