Error on Bluegenes

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

Error on Bluegenes

Paulo Nuin
Hi everyone

I am trying to setup a different default mine in Bluegenes, mainly changing to WormMine on the config.edn

 :bluegenes-default-service-root "http://im-dev1.wormbase.org

Deploying with lein dev and prod is fine when I keep the default parameters, but as soon as change this line, I get a series of CORS-related errors. I updated Tomcat’s web.xml to allow CORS, but I still see the same errors. Some examples are in the pic attached.


I tried the same configuration with a docker container created locally and setting -e BLUEGENES_DEFAULT_SERVICE_ROOT="http://im-dev1.wormbase.org

Is there anything I am missing in the configuration?

Thanks in advance

Cheers

Paulo







_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Error on Bluegenes

K.H. Reierskog

Hello Paulo,

Is wormmine accessible on http://im-dev1.wormbase.org or does it need the mine namespace path: http://im-dev1.wormbase.org/wormmine

Could you try setting the service root to that instead?

Cheers,

Kevin

On 1/14/21 3:25 AM, Paulo Nuin wrote:
Hi everyone

I am trying to setup a different default mine in Bluegenes, mainly changing to WormMine on the config.edn

 :bluegenes-default-service-root "http://im-dev1.wormbase.org

Deploying with lein dev and prod is fine when I keep the default parameters, but as soon as change this line, I get a series of CORS-related errors. I updated Tomcat’s web.xml to allow CORS, but I still see the same errors. Some examples are in the pic attached.


I tried the same configuration with a docker container created locally and setting -e BLUEGENES_DEFAULT_SERVICE_ROOT="http://im-dev1.wormbase.org

Is there anything I am missing in the configuration?

Thanks in advance

Cheers

Paulo







_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Error on Bluegenes

Paulo Nuin
Hi

The mine is accessible via the URL

http://im-dev1.wormbase.org

(This is our test/build instance)

Tomcat is behind a httpd proxy that redirects port 8000 to 80 and the full URL of the mine is

http://im-dev1.wormbase.org/tools/wormmine/begin.do

I got a fresh clone from Blugenes and tested all possibilities.


With

 :bluegenes-default-service-root "http://im-dev1.wormbase.org"

As in the previous email, I see a blank screen with the errors appearing in the console.


With

 :bluegenes-default-service-root "http://im-dev1.wormbase.org/tools”

I see a warning at the bottom of the screen, it seems the mine is loaded, but navigation is blocked

Failed to acquire token. It's likely that you have no connection to the InterMine instance.


With

:bluegenes-default-service-root "http://im-dev1.wormbase.org/tools/wormmine”


I see a number of errors

Failed assets/fetch-branding from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-web-service-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-summary-fields from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-intermine-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-release-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-widgets from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-class-keys from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-templates from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-model from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-lists from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
X
Failed assets/fetch-web-properties from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.


I guess the second option is the correct one. Now, what is the token issue?

Thanks a lot for all the help

Cheers

Paulo



> On Jan 14, 2021, at 2:49 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hello Paulo,
>
> Is wormmine accessible on http://im-dev1.wormbase.org or does it need the mine namespace path: http://im-dev1.wormbase.org/wormmine
>
> Could you try setting the service root to that instead?
>
> Cheers,
>
> Kevin
>
> On 1/14/21 3:25 AM, Paulo Nuin wrote:
>> Hi everyone
>>
>> I am trying to setup a different default mine in Bluegenes, mainly changing to WormMine on the config.edn
>>
>>  :bluegenes-default-service-root "http://im-dev1.wormbase.org”
>>
>> Deploying with lein dev and prod is fine when I keep the default parameters, but as soon as change this line, I get a series of CORS-related errors. I updated Tomcat’s web.xml to allow CORS, but I still see the same errors. Some examples are in the pic attached.
>>
>>
>> I tried the same configuration with a docker container created locally and setting -e BLUEGENES_DEFAULT_SERVICE_ROOT="http://im-dev1.wormbase.org”
>>
>> Is there anything I am missing in the configuration?
>>
>> Thanks in advance
>>
>> Cheers
>>
>> Paulo
>>
>>
>> <PastedGraphic-3.png>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> dev mailing list
>>
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Error on Bluegenes

K.H. Reierskog
I still think the proxy (or tomcat?) is not allowing connections from
localhost. Bluegenes will append /service and so on to
:bluegenes-default-service-root.

With the second option, it will block navigation as it hasn't managed to
connect to the mine. The token is to identify an anonymous user, and if
it fails to acquire, it usually means it didn't manage to connect to the
mine.

Did you try setting Access-Control-Allow-Origin to * ?

Cheers,

Kevin

On 1/14/21 4:17 PM, Paulo Nuin wrote:

> Hi
>
> The mine is accessible via the URL
>
> http://im-dev1.wormbase.org
>
> (This is our test/build instance)
>
> Tomcat is behind a httpd proxy that redirects port 8000 to 80 and the full URL of the mine is
>
> http://im-dev1.wormbase.org/tools/wormmine/begin.do
>
> I got a fresh clone from Blugenes and tested all possibilities.
>
>
> With
>
>  :bluegenes-default-service-root "http://im-dev1.wormbase.org"
>
> As in the previous email, I see a blank screen with the errors appearing in the console.
>
>
> With
>
>  :bluegenes-default-service-root "http://im-dev1.wormbase.org/tools”
>
> I see a warning at the bottom of the screen, it seems the mine is loaded, but navigation is blocked
>
> Failed to acquire token. It's likely that you have no connection to the InterMine instance.
>
>
> With
>
> :bluegenes-default-service-root "http://im-dev1.wormbase.org/tools/wormmine”
>
>
> I see a number of errors
>
> Failed assets/fetch-branding from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-web-service-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-summary-fields from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-intermine-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-release-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-widgets from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-class-keys from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-templates from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-model from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-lists from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
> X
> Failed assets/fetch-web-properties from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>
>
> I guess the second option is the correct one. Now, what is the token issue?
>
> Thanks a lot for all the help
>
> Cheers
>
> Paulo
>
>
>
>> On Jan 14, 2021, at 2:49 AM, K.H. Reierskog <[hidden email]> wrote:
>>
>> Hello Paulo,
>>
>> Is wormmine accessible on http://im-dev1.wormbase.org or does it need the mine namespace path: http://im-dev1.wormbase.org/wormmine
>>
>> Could you try setting the service root to that instead?
>>
>> Cheers,
>>
>> Kevin
>>
>> On 1/14/21 3:25 AM, Paulo Nuin wrote:
>>> Hi everyone
>>>
>>> I am trying to setup a different default mine in Bluegenes, mainly changing to WormMine on the config.edn
>>>
>>>  :bluegenes-default-service-root "http://im-dev1.wormbase.org”
>>>
>>> Deploying with lein dev and prod is fine when I keep the default parameters, but as soon as change this line, I get a series of CORS-related errors. I updated Tomcat’s web.xml to allow CORS, but I still see the same errors. Some examples are in the pic attached.
>>>
>>>
>>> I tried the same configuration with a docker container created locally and setting -e BLUEGENES_DEFAULT_SERVICE_ROOT="http://im-dev1.wormbase.org”
>>>
>>> Is there anything I am missing in the configuration?
>>>
>>> Thanks in advance
>>>
>>> Cheers
>>>
>>> Paulo
>>>
>>>
>>> <PastedGraphic-3.png>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>>
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Error on Bluegenes

Paulo Nuin
Hi

It might be some disconnection between the proxy in front of Tomcat. I added the related filters to Tomcat, I might need to check how httpd is configured.

I will keep trying, thanks.

Cheers

Paulo



> On Jan 14, 2021, at 9:39 AM, K.H. Reierskog <[hidden email]> wrote:
>
> I still think the proxy (or tomcat?) is not allowing connections from
> localhost. Bluegenes will append /service and so on to
> :bluegenes-default-service-root.
>
> With the second option, it will block navigation as it hasn't managed to
> connect to the mine. The token is to identify an anonymous user, and if
> it fails to acquire, it usually means it didn't manage to connect to the
> mine.
>
> Did you try setting Access-Control-Allow-Origin to * ?
>
> Cheers,
>
> Kevin
>
> On 1/14/21 4:17 PM, Paulo Nuin wrote:
>> Hi
>>
>> The mine is accessible via the URL
>>
>> http://im-dev1.wormbase.org
>>
>> (This is our test/build instance)
>>
>> Tomcat is behind a httpd proxy that redirects port 8000 to 80 and the full URL of the mine is
>>
>> http://im-dev1.wormbase.org/tools/wormmine/begin.do
>>
>> I got a fresh clone from Blugenes and tested all possibilities.
>>
>>
>> With
>>
>> :bluegenes-default-service-root "http://im-dev1.wormbase.org"
>>
>> As in the previous email, I see a blank screen with the errors appearing in the console.
>>
>>
>> With
>>
>> :bluegenes-default-service-root "http://im-dev1.wormbase.org/tools”
>>
>> I see a warning at the bottom of the screen, it seems the mine is loaded, but navigation is blocked
>>
>> Failed to acquire token. It's likely that you have no connection to the InterMine instance.
>>
>>
>> With
>>
>> :bluegenes-default-service-root "http://im-dev1.wormbase.org/tools/wormmine”
>>
>>
>> I see a number of errors
>>
>> Failed assets/fetch-branding from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-web-service-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-summary-fields from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-intermine-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-release-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-widgets from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-class-keys from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-templates from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-model from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-lists from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>> X
>> Failed assets/fetch-web-properties from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>
>>
>> I guess the second option is the correct one. Now, what is the token issue?
>>
>> Thanks a lot for all the help
>>
>> Cheers
>>
>> Paulo
>>
>>
>>
>>> On Jan 14, 2021, at 2:49 AM, K.H. Reierskog <[hidden email]> wrote:
>>>
>>> Hello Paulo,
>>>
>>> Is wormmine accessible on http://im-dev1.wormbase.org or does it need the mine namespace path: http://im-dev1.wormbase.org/wormmine
>>>
>>> Could you try setting the service root to that instead?
>>>
>>> Cheers,
>>>
>>> Kevin
>>>
>>> On 1/14/21 3:25 AM, Paulo Nuin wrote:
>>>> Hi everyone
>>>>
>>>> I am trying to setup a different default mine in Bluegenes, mainly changing to WormMine on the config.edn
>>>>
>>>> :bluegenes-default-service-root "http://im-dev1.wormbase.org”
>>>>
>>>> Deploying with lein dev and prod is fine when I keep the default parameters, but as soon as change this line, I get a series of CORS-related errors. I updated Tomcat’s web.xml to allow CORS, but I still see the same errors. Some examples are in the pic attached.
>>>>
>>>>
>>>> I tried the same configuration with a docker container created locally and setting -e BLUEGENES_DEFAULT_SERVICE_ROOT="http://im-dev1.wormbase.org”
>>>>
>>>> Is there anything I am missing in the configuration?
>>>>
>>>> Thanks in advance
>>>>
>>>> Cheers
>>>>
>>>> Paulo
>>>>
>>>>
>>>> <PastedGraphic-3.png>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>>
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Error on Bluegenes

Paulo Nuin
Hi

Thanks for all the help. I was able to solve my issues by changing the reverse proxy. I was using Apache and even with a top notch CORS setting, nothing was working.

For documentation, I changed to nginx and everything is working fine. I even noticed the new config.edn and I already used to modify some access things.

Cheers

Paulo

> On Jan 14, 2021, at 9:46 AM, Paulo Nuin <[hidden email]> wrote:
>
> Hi
>
> It might be some disconnection between the proxy in front of Tomcat. I added the related filters to Tomcat, I might need to check how httpd is configured.
>
> I will keep trying, thanks.
>
> Cheers
>
> Paulo
>
>
>
>> On Jan 14, 2021, at 9:39 AM, K.H. Reierskog <[hidden email]> wrote:
>>
>> I still think the proxy (or tomcat?) is not allowing connections from
>> localhost. Bluegenes will append /service and so on to
>> :bluegenes-default-service-root.
>>
>> With the second option, it will block navigation as it hasn't managed to
>> connect to the mine. The token is to identify an anonymous user, and if
>> it fails to acquire, it usually means it didn't manage to connect to the
>> mine.
>>
>> Did you try setting Access-Control-Allow-Origin to * ?
>>
>> Cheers,
>>
>> Kevin
>>
>> On 1/14/21 4:17 PM, Paulo Nuin wrote:
>>> Hi
>>>
>>> The mine is accessible via the URL
>>>
>>> http://im-dev1.wormbase.org
>>>
>>> (This is our test/build instance)
>>>
>>> Tomcat is behind a httpd proxy that redirects port 8000 to 80 and the full URL of the mine is
>>>
>>> http://im-dev1.wormbase.org/tools/wormmine/begin.do
>>>
>>> I got a fresh clone from Blugenes and tested all possibilities.
>>>
>>>
>>> With
>>>
>>> :bluegenes-default-service-root "http://im-dev1.wormbase.org"
>>>
>>> As in the previous email, I see a blank screen with the errors appearing in the console.
>>>
>>>
>>> With
>>>
>>> :bluegenes-default-service-root "http://im-dev1.wormbase.org/tools”
>>>
>>> I see a warning at the bottom of the screen, it seems the mine is loaded, but navigation is blocked
>>>
>>> Failed to acquire token. It's likely that you have no connection to the InterMine instance.
>>>
>>>
>>> With
>>>
>>> :bluegenes-default-service-root "http://im-dev1.wormbase.org/tools/wormmine”
>>>
>>>
>>> I see a number of errors
>>>
>>> Failed assets/fetch-branding from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-web-service-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-summary-fields from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-intermine-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-release-version from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-widgets from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-class-keys from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-templates from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-model from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-lists from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>> X
>>> Failed assets/fetch-web-properties from WormMine. Please contact the maintainers of the InterMine instance. BlueGenes may work in reduced capacity.
>>>
>>>
>>> I guess the second option is the correct one. Now, what is the token issue?
>>>
>>> Thanks a lot for all the help
>>>
>>> Cheers
>>>
>>> Paulo
>>>
>>>
>>>
>>>> On Jan 14, 2021, at 2:49 AM, K.H. Reierskog <[hidden email]> wrote:
>>>>
>>>> Hello Paulo,
>>>>
>>>> Is wormmine accessible on http://im-dev1.wormbase.org or does it need the mine namespace path: http://im-dev1.wormbase.org/wormmine
>>>>
>>>> Could you try setting the service root to that instead?
>>>>
>>>> Cheers,
>>>>
>>>> Kevin
>>>>
>>>> On 1/14/21 3:25 AM, Paulo Nuin wrote:
>>>>> Hi everyone
>>>>>
>>>>> I am trying to setup a different default mine in Bluegenes, mainly changing to WormMine on the config.edn
>>>>>
>>>>> :bluegenes-default-service-root "http://im-dev1.wormbase.org”
>>>>>
>>>>> Deploying with lein dev and prod is fine when I keep the default parameters, but as soon as change this line, I get a series of CORS-related errors. I updated Tomcat’s web.xml to allow CORS, but I still see the same errors. Some examples are in the pic attached.
>>>>>
>>>>>
>>>>> I tried the same configuration with a docker container created locally and setting -e BLUEGENES_DEFAULT_SERVICE_ROOT="http://im-dev1.wormbase.org”
>>>>>
>>>>> Is there anything I am missing in the configuration?
>>>>>
>>>>> Thanks in advance
>>>>>
>>>>> Cheers
>>>>>
>>>>> Paulo
>>>>>
>>>>>
>>>>> <PastedGraphic-3.png>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>>
>>>>> [hidden email]
>>>>> https://lists.intermine.org/mailman/listinfo/dev
>>
>

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev