(null):// header in visualisation links (IGV etc.)

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(null):// header in visualisation links (IGV etc.)

Lubos Klucar
When clicking dataset visualisation links (UCSC, IGV, IGB, bam.iobio bam.iobio.io ...) on my galaxy installation [20.09] I'm always getting error:

Error: (null)://mygalaxy.mydomain.org/display_application/3d954174ae8d....

When manually changing the link from "(null)://" to "https://" the link is fully functional.

Other links from galaxy interface (download icon for any dataset) works without any problems.

Any help would be highly appreciated!

best

Lubos
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Re: (null):// header in visualisation links (IGV etc.)

Lubos Klucar
Dear Helena,

thanks a lot, but I'm afraid this is not the case - 'RequestHeader' is
set as described.

It should be probably some trivial mistake hidden somewhere in the
config files, which enable/disable a proper construction of URL text
string. I was looking everywhere, but still no luck.

best

Lubos

On 14/04/2021 10:40, Helena Rasche wrote:

> Your proxy might not be forwarding the protocol if that's the issue
> you're seeing.
>
> e.g. for apache, https://docs.galaxyproject.org/en/master/admin/apache.html
>
>      # Galaxy needs to know that this is https for generating URLs
>      RequestHeader  set X-URL-SCHEME"%{REQUEST_SCHEME}e" Hope that helps, Ciao
>
> On 14/04/2021 10:38, [hidden email] wrote:
>> When clicking dataset visualisation links (UCSC, IGV, IGB, bam.iobio bam.iobio.io ...) on my galaxy installation [20.09] I'm always getting error:
>>
>> Error: (null)://mygalaxy.mydomain.org/display_application/3d954174ae8d....
>>
>> When manually changing the link from "(null)://" to "https://" the link is fully functional.
>>
>> Other links from galaxy interface (download icon for any dataset) works without any problems.
>>
>> Any help would be highly appreciated!
>>
>> best
>>
>> Lubos
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>    %(web_page_url)s
>>
>> To search Galaxy mailing lists use the unified search at:
>>    http://galaxyproject.org/search/

--

                 Lubos Klucar

                 Institute of Molecular Biology
                 Slovak Academy of Science
                 Dubravska cesta 21
                 845 51  Bratislava 45
                 Slovakia

                 Tel.: +421 2 5930 7413
                 Fax.: +421 2 5930 7416
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Re: (null):// header in visualisation links (IGV etc.)

Martin Čech
Lubos, do you have an opportunity to disable the proxy for a bit? So we can narrow down the suspects. 
Martin

On Wed, Apr 14, 2021 at 11:22 AM Lubos Klucar <[hidden email]> wrote:
Dear Helena,

thanks a lot, but I'm afraid this is not the case - 'RequestHeader' is
set as described.

It should be probably some trivial mistake hidden somewhere in the
config files, which enable/disable a proper construction of URL text
string. I was looking everywhere, but still no luck.

best

Lubos

On 14/04/2021 10:40, Helena Rasche wrote:
> Your proxy might not be forwarding the protocol if that's the issue
> you're seeing.
>
> e.g. for apache, https://docs.galaxyproject.org/en/master/admin/apache.html
>
>      # Galaxy needs to know that this is https for generating URLs
>      RequestHeader  set X-URL-SCHEME"%{REQUEST_SCHEME}e" Hope that helps, Ciao
>
> On 14/04/2021 10:38, [hidden email] wrote:
>> When clicking dataset visualisation links (UCSC, IGV, IGB, bam.iobio bam.iobio.io ...) on my galaxy installation [20.09] I'm always getting error:
>>
>> Error: (null)://mygalaxy.mydomain.org/display_application/3d954174ae8d....
>>
>> When manually changing the link from "(null)://" to "https://" the link is fully functional.
>>
>> Other links from galaxy interface (download icon for any dataset) works without any problems.
>>
>> Any help would be highly appreciated!
>>
>> best
>>
>> Lubos
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>    %(web_page_url)s
>>
>> To search Galaxy mailing lists use the unified search at:
>>    http://galaxyproject.org/search/

--

                 Lubos Klucar

                 Institute of Molecular Biology
                 Slovak Academy of Science
                 Dubravska cesta 21
                 845 51  Bratislava 45
                 Slovakia

                 Tel.: +421 2 5930 7413
                 Fax.: +421 2 5930 7416
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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___________________________________________________________
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Re: (null):// header in visualisation links (IGV etc.)

Lubos Klucar
Uff, I'll try that, though it will take some time since I have to figure out what in my apache config belongs to the proxying and what to the standard ssl virtualhost config...

Lubos
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Re: (null):// header in visualisation links (IGV etc.)

Martin Čech
I don't know your setup but maybe you could serve Galaxy on a different port without Apache/ssl to test.
M.

On Wed, Apr 14, 2021 at 11:58 AM <[hidden email]> wrote:
Uff, I'll try that, though it will take some time since I have to figure out what in my apache config belongs to the proxying and what to the standard ssl virtualhost config...

Lubos
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Re: (null):// header in visualisation links (IGV etc.)

Lubos Klucar
Thanks for the hint!

After disabling the proxy, the links are properly formatted (though IGV
has reported some error after importing my example BAM file).

Something is wrong with my proxy setup then? If needed, I happy to post
(parts) of my config files.

best

Lubos



On 14/04/2021 12:07, Martin Čech wrote:

> I don't know your setup but maybe you could serve Galaxy on a different
> port without Apache/ssl to test.
> M.
>
> On Wed, Apr 14, 2021 at 11:58 AM <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Uff, I'll try that, though it will take some time since I have to
>     figure out what in my apache config belongs to the proxying and what
>     to the standard ssl virtualhost config...
>
>     Lubos
>     ___________________________________________________________
>     Please keep all replies on the list by using "reply all"
>     in your mail client.  To manage your subscriptions to this
>     and other Galaxy lists, please use the interface at:
>        %(web_page_url)s
>
>     To search Galaxy mailing lists use the unified search at:
>     http://galaxyproject.org/search/ <http://galaxyproject.org/search/>
>
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