Json API docs

[gitoliver]

Tool: Json API using the docs here: https://github.com/GLYCAM-Web/website/blob/master/Examples/JsonApi/README.md

Bug Description: I'm getting failed connections when using the documents provided:

oliver@frankus:~/Downloads$ bash api-https.bash build-sequence.json www.glycam.org
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 3.33.152.147:443...
* TCP_NODELAY set
  0     0    0     0    0     0      0      0 --:--:--  0:02:09 --:--:--     0* connect to 3.33.152.147 port 443 failed: Connection timed out
*   Trying 15.197.142.173:443...
* TCP_NODELAY set
  0     0    0     0    0     0      0      0 --:--:--  0:03:34 --:--:--     0* After 85261ms connect time, move on!
* connect to 15.197.142.173 port 443 failed: Connection timed out
* Failed to connect to www.glycam.org port 443: Connection timed out
  0     0    0     0    0     0      0      0 --:--:--  0:03:34 --:--:--     0
* Closing connection 0
curl: (28) Failed to connect to www.glycam.org port 443: Connection timed out
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0*   Trying 15.197.142.173:443...

Also, the docs are not directing me to download min-gas.pdb, but instead molecule.pdb. Users will definitely want min-gas.pdb unless they know better.

[danwentworthart]

Could not yet determine why the server rejects the connection, suspect recent changes to server config need re-examining. I did go ahead and replace the 'molecule.db' with 'min-gas.pdb'.

[danwentworthart]

Did some more testing. I am still failing to find errors... Probably looking in the wrong place. However, I did replicate the issue, and can add that this is intermittent. It does return responses in some cases, but also fails to respond in other cases. I have seen an alternating pattern. Within the span of about an hour, I failed, succeeded, failed again, and succeeded again, in that order. If I can spot a useful log, I will attach it here.

[Lachele]

I don't know what else might be happening, but you definitely cannot use www.glycam.org as the URL.

bash api-https.bash build-sequence.json glycam.org

I have opened a ticket for this.

@danwentworthart - were you using glycam.org or www.glycam.org?

[Lachele]

Using a script and glycam.org (not with the www), I just got 20 successful API requests in a row. I added a 1 second sleep between each, but I don't expect that matters.