URL prefix doesn't work properly in Galaxy v18.09

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URL prefix doesn't work properly in Galaxy v18.09

Ping Luo
I configured URL prefix in galaxy 18.09. It has problems of resolving some of the links, including:
 
     workflow
     visualize -> create visualization
     shared data -> workflows
     shared data -> visualizations

I will use workflow as an example to illustrate what happens. When the mouse cursor is put on workflow, the URL shown in at the left bottom of the browser shows

     https://xxx.xxx.tamu.edu/galaxy/workflows/list

But after I clicked 'workflow', the real URL shown in the address bar is actually  

Of course, there is no such a page and the browser shows a blank page. If I manually remove one galaxy in the URL, the page is correctly shown.

Beside the four mentioned above, other links work fine. If galaxy is configured without prefix, then there is no problem.

 I also tested v18.05. With all the configuration being the same, this version doesn't have the problem with prefix like v18.09 does. So I think this is a bug in v18.09 with URL prefix.

Ping

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Re: URL prefix doesn't work properly in Galaxy v18.09

Peter Briggs
Hello Ping (and Galaxy-devs)

Did this get resolved? We are still on 18.09 and serving our production instance with a proxy prefix, and one of my users has hit this issue when trying to access the "Workflows" tab from the main page.

As Ping says, it appears that Galaxy is inserting an extra copy of the prefix into the target URL - if the user removes this manually then the page loads okay.

Does anyone know, is there a fix for this in 18.09?

Thanks!

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

________________________________
From: galaxy-dev [[hidden email]] on behalf of Ping Luo [[hidden email]]
Sent: Monday, December 17, 2018 9:04 PM
To: galaxy-dev
Subject: [galaxy-dev] URL prefix doesn't work properly in Galaxy v18.09

I configured URL prefix in galaxy 18.09. It has problems of resolving some of the links, including:

     workflow
     visualize -> create visualization
     shared data -> workflows
     shared data -> visualizations

I will use workflow as an example to illustrate what happens. When the mouse cursor is put on workflow, the URL shown in at the left bottom of the browser shows

     https://xxx.xxx.tamu.edu/galaxy/workflows/list

But after I clicked 'workflow', the real URL shown in the address bar is actually

    https://xxx.xxxx.tamu.edu/galaxy/galaxy//workflows/list?__identifer=sk0xsywiqrs

Of course, there is no such a page and the browser shows a blank page. If I manually remove one galaxy in the URL, the page is correctly shown.

Beside the four mentioned above, other links work fine. If galaxy is configured without prefix, then there is no problem.

 I also tested v18.05. With all the configuration being the same, this version doesn't have the problem with prefix like v18.09 does. So I think this is a bug in v18.09 with URL prefix.

Ping
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Re: URL prefix doesn't work properly in Galaxy v18.09

Peter Briggs
Replying to my own message in case it's of use to someone else:

It looks like this can be fixed by commenting out the 'target: "__use_router__"' lines in client/galaxy/scripts/layout/menu.js i.e.

diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js
index 2dc1b41098..2d4c1db8c7 100644
--- a/client/galaxy/scripts/layout/menu.js
+++ b/client/galaxy/scripts/layout/menu.js
@@ -46,7 +46,8 @@ var Collection = Backbone.Collection.extend({
             tooltip: _l("Chain tools into workflows"),
             disabled: !Galaxy.user.id,
             url: "workflows/list",
-            target: "__use_router__"
+            //PJB remove target as it seems to break when using proxy-prefix
+            //target: "__use_router__"
         });
 
         //
@@ -61,7 +62,8 @@ var Collection = Backbone.Collection.extend({
                 {
                     title: _l("Create Visualization"),
                     url: "visualizations",
-                    target: "__use_router__"
+                    //PJB remove target as it seems to break when using proxy-prefix
+                    //target: "__use_router__"
                 },
                 {
                     title: _l("Interactive Environments"),

(I needed to recompile the packed Javascript afterwards by running the common_startup.sh script before the changes appeared in the web interface.)

This appears to fix the links to "Workflows" and "Visualisations" in the masthead of the main page.

HTH

Best wishes

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


________________________________________
From: Peter Briggs [[hidden email]]
Sent: Thursday, May 16, 2019 2:01 PM
To: Ping Luo; galaxy-dev
Subject: [galaxy-dev] Re: URL prefix doesn't work properly in Galaxy v18.09

Hello Ping (and Galaxy-devs)

Did this get resolved? We are still on 18.09 and serving our production instance with a proxy prefix, and one of my users has hit this issue when trying to access the "Workflows" tab from the main page.

As Ping says, it appears that Galaxy is inserting an extra copy of the prefix into the target URL - if the user removes this manually then the page loads okay.

Does anyone know, is there a fix for this in 18.09?

Thanks!

Peter

--
Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

________________________________
From: galaxy-dev [[hidden email]] on behalf of Ping Luo [[hidden email]]
Sent: Monday, December 17, 2018 9:04 PM
To: galaxy-dev
Subject: [galaxy-dev] URL prefix doesn't work properly in Galaxy v18.09

I configured URL prefix in galaxy 18.09. It has problems of resolving some of the links, including:

     workflow
     visualize -> create visualization
     shared data -> workflows
     shared data -> visualizations

I will use workflow as an example to illustrate what happens. When the mouse cursor is put on workflow, the URL shown in at the left bottom of the browser shows

     https://xxx.xxx.tamu.edu/galaxy/workflows/list

But after I clicked 'workflow', the real URL shown in the address bar is actually

    https://xxx.xxxx.tamu.edu/galaxy/galaxy//workflows/list?__identifer=sk0xsywiqrs

Of course, there is no such a page and the browser shows a blank page. If I manually remove one galaxy in the URL, the page is correctly shown.

Beside the four mentioned above, other links work fine. If galaxy is configured without prefix, then there is no problem.

 I also tested v18.05. With all the configuration being the same, this version doesn't have the problem with prefix like v18.09 does. So I think this is a bug in v18.09 with URL prefix.

Ping
___________________________________________________________
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/
___________________________________________________________
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/
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Re: URL prefix doesn't work properly in Galaxy v18.09

Ping Luo
Peter,

Thanks for the fix. We will try it on our galaxy.

Best,

Ping

On Thu, May 16, 2019 at 9:01 AM Peter Briggs <[hidden email]>
wrote:

> Replying to my own message in case it's of use to someone else:
>
> It looks like this can be fixed by commenting out the 'target:
> "__use_router__"' lines in client/galaxy/scripts/layout/menu.js i.e.
>
> diff --git a/client/galaxy/scripts/layout/menu.js
> b/client/galaxy/scripts/layout/menu.js
> index 2dc1b41098..2d4c1db8c7 100644
> --- a/client/galaxy/scripts/layout/menu.js
> +++ b/client/galaxy/scripts/layout/menu.js
> @@ -46,7 +46,8 @@ var Collection = Backbone.Collection.extend({
>              tooltip: _l("Chain tools into workflows"),
>              disabled: !Galaxy.user.id,
>              url: "workflows/list",
> -            target: "__use_router__"
> +            //PJB remove target as it seems to break when using
> proxy-prefix
> +            //target: "__use_router__"
>          });
>
>          //
> @@ -61,7 +62,8 @@ var Collection = Backbone.Collection.extend({
>                  {
>                      title: _l("Create Visualization"),
>                      url: "visualizations",
> -                    target: "__use_router__"
> +                    //PJB remove target as it seems to break when using
> proxy-prefix
> +                    //target: "__use_router__"
>                  },
>                  {
>                      title: _l("Interactive Environments"),
>
> (I needed to recompile the packed Javascript afterwards by running the
> common_startup.sh script before the changes appeared in the web interface.)
>
> This appears to fix the links to "Workflows" and "Visualisations" in the
> masthead of the main page.
>
> HTH
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs [hidden email]
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
>
> ________________________________________
> From: Peter Briggs [[hidden email]]
> Sent: Thursday, May 16, 2019 2:01 PM
> To: Ping Luo; galaxy-dev
> Subject: [galaxy-dev] Re: URL prefix doesn't work properly in Galaxy v18.09
>
> Hello Ping (and Galaxy-devs)
>
> Did this get resolved? We are still on 18.09 and serving our production
> instance with a proxy prefix, and one of my users has hit this issue when
> trying to access the "Workflows" tab from the main page.
>
> As Ping says, it appears that Galaxy is inserting an extra copy of the
> prefix into the target URL - if the user removes this manually then the
> page loads okay.
>
> Does anyone know, is there a fix for this in 18.09?
>
> Thanks!
>
> Peter
>
> --
> Peter Briggs [hidden email]
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
> ________________________________
> From: galaxy-dev [[hidden email]] on behalf
> of Ping Luo [[hidden email]]
> Sent: Monday, December 17, 2018 9:04 PM
> To: galaxy-dev
> Subject: [galaxy-dev] URL prefix doesn't work properly in Galaxy v18.09
>
> I configured URL prefix in galaxy 18.09. It has problems of resolving some
> of the links, including:
>
>      workflow
>      visualize -> create visualization
>      shared data -> workflows
>      shared data -> visualizations
>
> I will use workflow as an example to illustrate what happens. When the
> mouse cursor is put on workflow, the URL shown in at the left bottom of the
> browser shows
>
>      https://xxx.xxx.tamu.edu/galaxy/workflows/list
>
> But after I clicked 'workflow', the real URL shown in the address bar is
> actually
>
>
> https://xxx.xxxx.tamu.edu/galaxy/galaxy//workflows/list?__identifer=sk0xsywiqrs
>
> Of course, there is no such a page and the browser shows a blank page. If
> I manually remove one galaxy in the URL, the page is correctly shown.
>
> Beside the four mentioned above, other links work fine. If galaxy is
> configured without prefix, then there is no problem.
>
>  I also tested v18.05. With all the configuration being the same, this
> version doesn't have the problem with prefix like v18.09 does. So I think
> this is a bug in v18.09 with URL prefix.
>
> Ping
> ___________________________________________________________
> 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/
>
___________________________________________________________
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/