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
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
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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 failedUncaught 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-JacksonGalaxy Application Supporthttp://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 ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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/fe6d22e1a7e4e6d38b15f4128554783... 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
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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_lin.... 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/fe6d22e1a7e4e6d38b15f4128554783...
Probably Sam (Aysam) can give you more practical advice (CC'd)?
Peter
I am making some clickable buttons in the home page of my instance
On Mon, Feb 29, 2016 at 12:29 PM, Makis Ladoukakis <makis4ever@hotmail.com> wrote: 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
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Thanks a lot Peter and Aysam! The fix worked perfectly! Regards, Makis Date: Mon, 29 Feb 2016 22:18:37 -0500 Subject: Re: [galaxy-dev] Downgrade tool upload tool From: aysam.guerler@gmail.com To: p.j.a.cock@googlemail.com CC: makis4ever@hotmail.com; jen@galaxyproject.org; galaxy-dev@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org 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_lin.... 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/fe6d22e1a7e4e6d38b15f4128554783... 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
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
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
___________________________________________________________
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:
To search Galaxy mailing lists use the unified search at:
___________________________________________________________
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:
To search Galaxy mailing lists use the unified search at:
participants (4)
-
Aysam Guerler -
Jennifer Hillman-Jackson -
Makis Ladoukakis -
Peter Cock