Thanks Peter. I think you are right and that its a change in Galaxy which causes this routing issue. I have prepared a fix for it: https://github.com/galaxyproject/galaxy/compare/dev...guerler:fix_upload_link_000?expand=1. Ill double check tomorrow with those working on the routing and then issue a PR. Thanks a lot for reporting this Makis.

On Mon, Feb 29, 2016 at 8:17 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Thanks for clarifying Makis,

I think this change is likely due to changes in Galaxy rather than
in the upload tool itself. On our (slightly out of date) Galaxy or the
public server, that URL no longer loads the original tool form -
you get the new drag-and-drop upload interface.

I would guess some of the special case code like this matters:
https://github.com/galaxyproject/galaxy/blob/fe6d22e1a7e4e6d38b15f4128554783765bc69a1/client/galaxy/scripts/mvc/tool/tools.js#L525

Probably Sam (Aysam) can give you more practical advice (CC'd)?

Peter

On Mon, Feb 29, 2016 at 12:29 PM, Makis Ladoukakis
<makis4ever@hotmail.com> wrote:
> I am making some clickable buttons in the home page of my instance through a
> java script that is called from the welcome.html file. These buttons
> correspond to my most used tools. For example I have a section like this:
>
> <div align="center" class="container">
> <div id='nested_container'>
> <ul class='list'>
>
>             <li class='item'>
>                     <div class='my_class_main'><img
> src="feimg/GetData.gif"/></div>
>                     <ul class="sublist">
>                         <li class="subitem"><div class='my_class_sub'><a
> href="http://myserver/galaxy/tool_runner?tool_id=upload1"
> target="_parent"><img src="feimg/Upload.gif" width=250%
> height=300%/></a></div></li>
>                         <li class="subitem"><div class='my_class_sub'><a
> href="http://myserver/galaxy/library/browse_libraries" target="_parent"><img
> src="feimg/Libraries.gif" width=250% height=300%/></a></div></li>
>                     </ul>
>                 </li>
>             </ul>
>         </div>
>   </div>
>
> indicating two buttons one for the upload tool and one for the libraries.
> The libraries button work but when I click on the button for the upload tool
> the webpage just refreshes instead of opening the tool. This worked
> perfectly with the previous version of the upload tool and I was thinking
> how to get it back.
>
> Thank you,
> Makis
>
>
>> Date: Mon, 29 Feb 2016 11:39:26 +0000
>> Subject: Re: [galaxy-dev] Downgrade tool upload tool
>> From: p.j.a.cock@googlemail.com
>> To: makis4ever@hotmail.com
>> CC: jen@galaxyproject.org; galaxy-dev@lists.bx.psu.edu;
>> galaxy-dev@lists.galaxyproject.org
>
>>
>> Hi Makis,
>>
>> The upload tool is a little special in that it is used internally by
>> Galaxy and doesn't entirely behave like a normal tool.
>>
>> What are you trying to achieve by "downgrading" it?
>>
>> Peter
>>
>> On Mon, Feb 29, 2016 at 11:29 AM, Makis Ladoukakis
>> <makis4ever@hotmail.com> wrote:
>> > What about if I used a second "tool upload" tool? I took the python
>> > script
>> > from an earlier version and named it upload_old.py and did the same for
>> > the
>> > xml file (upload.xml -> upload_old.xml) while changing the latter to
>> > call
>> > the new python script. Nevertheless when I did that and tried to run it
>> > I
>> > got a popup window with the following error:
>> >
>> > Tool request failed
>> >
>> > Uncaught exception in exposed API method:
>> >
>> >
>> > Is there a way to make this work? Or maybe another workaround?
>> >
>> > Thank you in advance,
>> > Makis
>> >
>> >
>> >
>> > ________________________________
>> > From: jen@galaxyproject.org
>> > Date: Fri, 26 Feb 2016 10:22:44 -0800
>> > Subject: Re: [galaxy-dev] Downgrade tool upload tool
>> > To: makis4ever@hotmail.com
>> > CC: galaxy-dev@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org
>> >
>> >
>> > Hello,
>> >
>> > The Upload tool is a direct component of Galaxy. To use an earlier
>> > version
>> > of the tool, I believe that you would have to run an earlier version of
>> > Galaxy.
>> >
>> > Others here can amend this, if they know of an alternative.
>> >
>> > Thanks,
>> >
>> > Jen
>> >
>> > --
>> > Jennifer Hillman-Jackson
>> > Galaxy Application Support
>> > http://usegalaxy.org
>> > http://galaxyproject.org
>> > http://biostar.usegalaxy.org
>> >
>> >
>> > On Fri, Feb 26, 2016 at 4:01 AM, Makis Ladoukakis
>> > <makis4ever@hotmail.com>
>> > wrote:
>> >
>> > Hello everyone,
>> >
>> > I was wondering whether it's possible to downgrade the upload tool to
>> > the
>> > previous version(1.1.4).
>> >
>> > I copied the upload.py and upload.xml scripts from a previous galaxy
>> > version
>> > to the tools/data_source/ directory and reloaded the tool as admin but
>> > it
>> > hasn't changed even when I restarted the server.
>> >
>> > Do I have to change something else in addition?
>> >
>> > Thank you,
>> > Makis
>> >
>> > ___________________________________________________________
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>> >
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