StringApp cannot connect to server - Proxy issue?

[Stefan]

Hi,

I am using Cytoscape 3.7.1 with String 1.4.2. There seems to be an issue for the string app connecting to the internet.
We are using a proxy in our university. I already managed to configure the settings in Cytoscape, so it can connect (ie: Appstore and IntAct works). It still seems to be an issue for String to connect.
Following can be read in the task history:
"Getting annotations
 Query returned no terms
 URL: http://version11.string-db.org/api/json/get_string_ids?species=9606&caller_identity=string_app_v1_4_2&identifiers=Q99805
 Unexpected error when parsing JSON from server: Connect to version11.string-db.org:80 [version11.string-db.org/104.20.238.26, version11.string-db.org/104.20.239.26] failed: Connection timed out: connect
 URL:http://viruses.string-db.org/cgi/webservice_handler.pl?species=9606&caller_identity=string_app_v1_4_2&identifiers=Q99805
 Unexpected error when parsing JSON from server: Connect to viruses.string-db.org:80 [viruses.string-db.org/130.226.24.68] failed: Connection timed out: connect"

I also already checked the proxy configurations for java and they are fine.

Any suggestion is appreciated.
Cheers,
Stefan

[Scooter Morris]

Hi Stefan,

    We've never tested the StringApp with a proxy server.  We're just about ready to release StringApp 1.5, so we'll try to take a look at this before the release.

-- scooter

[stefan....@gmail.com]

Hi Scooter,
thank you for your effort. For now, I solved the problem by buying a WIFI adapter and connect to eduroam. That way it works ;-)

Cheers,
Stefan

[sophie.jamet]

Hi,

I have the same issue at my research institute, the protein query would not work and return the same error as Stefan.

I hope the new release will solve it!

Best

Sophie

[Lars Juhl Jensen]

Dear all,

I'm sorry to say that there is probably not much we can do to fix this at our end. The server is up and fully responsive. The problem is that the firewalls at some institutions block the outgoing requests, either on the individual computers or more often network-wide. In either case, it means that the queries never get to us. There are sadly only three solutions that I can think of:

1. If the blocking is done on the individual computer, get it configured so that Cytoscape is allowed to send requests.
2. If it is done on the network level, convince your network administrators to not block outgoing requests.
3. Use a VPN service to tunnel the traffic out through the firewall.

So far every case that I have seen of this was related to network traffic being blocked at the client end. I don't see how we would be able to solve that in Cytoscape or stringApp in a general way, but I would love to be proven wrong.

Best,

Lars

[Sophie Jamet]

Hi Lars,

thank you for your message, I will forward this to my IT department.

Of note, all other queries work for me, I have issues only with the protein query, and when I try the URL on my browser it works fine, the request get send. But I agree most likely it is on our end.

Best regards

Sophie

On Fri, Jun 21, 2019 at 2:23 AM Lars Juhl Jensen <lars.juh...@gmail.com> wrote:

Dear all,

I'm sorry to say that there is probably not much we can do to fix this at our end. The server is up and fully responsive. The problem is that the firewalls at some institutions block the outgoing requests, either on the individual computers or more often network-wide. In either case, it means that the queries never get to us. There are sadly only three solutions that I can think of:

1. If the blocking is done on the individual computer, get it configured so that Cytoscape is allowed to send requests.
2. If it is done on the network level, convince your network administrators to not block outgoing requests.
3. Use a VPN service to tunnel the traffic out through the firewall.

So far every case that I have seen of this was related to network traffic being blocked at the client end. I cannot think of any way that Cytoscape or the stringApp can work around that — arguably, it would be a security vulnerability if we were able to do that.

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[Lars Juhl Jensen]

Hi Sophie,

We now have a beta version of stringApp version 1.5, which will make use of any proxy server configured in Cytoscape. If you get in touch with us, you are welcome to test it and see if it fixes your issues. We know that the proxy code works per se (when we configure a proxy, the server gets the requests from the proxy), but we have no way of knowing if it fixes the problem for you. It would thus be great if you could help us test before we release it.

BW

Lars

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[Manut...@hotmail.com]

Le lundi 1 juillet 2019 13:56:32 UTC+2, Lars Juhl Jensen a écrit :
> Hi Sophie,
>
>
> We now have a beta version of stringApp version 1.5, which will make use of any proxy server configured in Cytoscape. If you get in touch with us, you are welcome to test it and see if it fixes your issues. We know that the proxy code works per se (when we configure a proxy, the server gets the requests from the proxy), but we have no way of knowing if it fixes the problem for you. It would thus be great if you could help us test before we release it.
>
>
> BW
> Lars
>
> On Friday, June 21, 2019 at 6:00:08 PM UTC+2, sophie.jamet wrote:
>
>
> Hi Lars,
> thank you for your message, I will forward this to my IT department.
> Of note, all other queries work for me, I have issues only with the protein query, and when I try the URL on my browser it works fine, the request get send. But I agree most likely it is on our end.
> Best regards
> Sophie
>
>
>
>
>
>
>
>
>
>
> On Fri, Jun 21, 2019 at 2:23 AM Lars Juhl Jensen <lars.ju...@gmail.com> wrote:
>
> Dear all,
>
>
> I'm sorry to say that there is probably not much we can do to fix this at our end. The server is up and fully responsive. The problem is that the firewalls at some institutions block the outgoing requests, either on the individual computers or more often network-wide. In either case, it means that the queries never get to us. There are sadly only three solutions that I can think of:

> If the blocking is done on the individual computer, get it configured so that Cytoscape is allowed to send requests.If it is done on the network level, convince your network administrators to not block outgoing requests.Use a VPN service to tunnel the traffic out through the firewall.

> To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.

>
> To post to this group, send email to cytoscape...@googlegroups.com.
>
> Visit this group at https://groups.google.com/group/cytoscape-helpdesk.
>
> To view this discussion on the web visit https://groups.google.com/d/msgid/cytoscape-helpdesk/ae3bac69-5e73-4f49-94fc-04d3c2b14eb1%40googlegroups.com.
>
> For more options, visit https://groups.google.com/d/optout.

Hi,
I have the same issue then Sophie with Proxy access. Did you get any positive update on this situation since this subject was posted?
Best regrads,
Manutea Serrero