10 Minute time limit about jgi-query HOT 7 CLOSED

@ncolaian,

So, is the request timing out while processing the XML file, or while downloading data files? Can you provide me with the query you're using?

It's not a built-in limit that I've imposed, and there doesn't seem to be anything in the cURL documentation suggesting a timeout once a connection has actually been established with the host. It's possible that cURL is unable to reach the server and is timing out for that reason, but I'd have to try it myself to figure that out.

from jgi-query.

The request times out while processing the XML file. I have been querying the fungal database (Using fungi as my query). The weird part about the time out is that it will work if it takes under 10 minutes, however if it reaches the 10 minute point it will produce an error every single time.

from jgi-query.

@ncolaian can you please provide the exact error output that you're getting? I can't recreate it on my end, perhaps due to higher bandwidth. Thanks!

from jgi-query.

The internet seems to be working well today, and I haven't received the same error yet because I haven't hit the 10 minute mark when running the query. If it happens again though I will post the error.

-ncolaian

From: Graham [email protected]
Sent: Saturday, July 16, 2016 8:21:19 PM
To: glarue/jgi-query
Cc: Colaianni, Nick Robert; Mention
Subject: Re: [glarue/jgi-query] 10 Minute time limit (#3)

@ncolaianhttps://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fgithub.com%2fncolaian&data=01%7c01%7cncolaian%40email.unc.edu%7c3c90009eb64944cd210d08d3add8466b%7c58b3d54f16c942d3af081fcabd095666%7c1&sdata=0j7K1n%2fW7EJBwlrcswSOX%2b%2bufkqN7UAQkf5SlbFqlpg%3d can you please provide the exact error output that you're getting? I can't recreate it on my end, perhaps due to higher bandwidth. Thanks!

You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fgithub.com%2fglarue%2fjgi-query%2fissues%2f3%23issuecomment-233158104&data=01%7c01%7cncolaian%40email.unc.edu%7c3c90009eb64944cd210d08d3add8466b%7c58b3d54f16c942d3af081fcabd095666%7c1&sdata=9BreocBmI6U1vhxmJOlF24klRkAzMmW4Wq%2bnzEzW%2f9U%3d, or mute the threadhttps://na01.safelinks.protection.outlook.com/?url=https%3a%2f%2fgithub.com%2fnotifications%2funsubscribe-auth%2fATg5Nh9o4lywP4JdOJqL0iUJkdPFNKhIks5qWXV_gaJpZM4JMlSi&data=01%7c01%7cncolaian%40email.unc.edu%7c3c90009eb64944cd210d08d3add8466b%7c58b3d54f16c942d3af081fcabd095666%7c1&sdata=U3Cz5npCoivXMQRlUOoLdgsSW2I48yj3501JMtUS2bc%3d.

from jgi-query.

@ncolaian okay please do, as it's likely to affect someone else is the future. Closing for now.

from jgi-query.

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 107 0 107 0 0 139 0 --:--:-- --:--:-- --:--:-- 104k
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 441 0 441 0 0 0 0 --:--:-- 0:10:00 --:--:-- 107
Cannot parse XML file or no organism match found.
Ensure remote file exists and has content at the following address:
http://genome.jgi.doe.gov/ext-api/downloads/get-directory?organism=fungi
Removing temp files and exiting

Here is the error.

from jgi-query.

Hey @ncolaian, see my recent commit moving the queries from http to https; it may help with the problem you were having.

from jgi-query.