Re: [galaxy-dev] Fwd: New galaxy parameter type

2016-07-20 Thread Mohamed Kassam 
Dear all,
I did not want to open a new subject, because I have the same problem.

I tried to follow what is was described here
https://github.com/galaxyproject/galaxy/pull/393, I add the lines a
described in the github, but when I am clicking to my tool I got

[image: Images intégrées 1]

And if i check the error in commad line I have

galaxy.web.framework.decorators ERROR 2016-07-20 10:05:44,357 Uncaught
exception in exposed API method:
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/lib/galaxy/web/framework/decorators.py",
line 258, in decorator
rval = func( self, trans, *args, **kwargs)
  File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py",
line 100, in build
return tool.to_json(trans, kwd.get('inputs', kwd))
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2383,
in to_json
populate_state(trans, self.inputs, state_inputs, state_errors,
params.__dict__)
  File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2255,
in populate_state
state[input.name] = input.get_initial_value(trans, context,
history=history)
TypeError: get_initial_value() got an unexpected keyword argument 'history'
10.38.149.37 - - [20/Jul/2016:10:05:44 +0200] "GET
/api/tools/irods_pull_main/build HTTP/1.1" 500 - "http://10.38.152.152:8080/;
"Mozilla/5.0 (Windows NT 6.1) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/51.0.2704.103 Safari/537.36"



Maybe something to add for the new version of galaxy ?


Thanks in advance,

Mohamed

2016-07-15 21:54 GMT+02:00 Martin Čech :

> forwarding to the list
>
>
> -- Forwarded message -
> From: Katherine Beaulieu 
> Date: Fri, Jul 15, 2016 at 3:45 PM
> Subject: Re: [galaxy-dev] New galaxy parameter type
> To: Martin Čech 
>
>
> Thanks Peter, I will look into that. The reason I am asking is because of
> what Mohammed asked earlier as well. I developed two tools which allow you
> to import and export information from a program called irods but you need
> to be able to authenticate with irods to be able to do so. Thanks again for
> always being helpful!
>
> On Fri, Jul 15, 2016 at 3:10 PM, Martin Čech  wrote:
>
>> Katherine please disregard my answer, I probably misread your question. :)
>> M.
>>
>> On Fri, Jul 15, 2016 at 3:05 PM Peter Cock 
>> wrote:
>>
>>> Did you mean parameter as in input field shown
>>> to the user? Like a combobox or text field?
>>>
>>> Since this happened to come up earlier today, here's
>>> a rejected pull request which added a password
>>> parameter - that ought to give you a rough idea:
>>>
>>> https://github.com/galaxyproject/galaxy/pull/393
>>>
>>> Peter
>>>
>>> On Fri, Jul 15, 2016 at 7:46 PM, Katherine Beaulieu
>>>  wrote:
>>> > Hi everyone,
>>> > I am looking to implement a new parameter type for galaxy tool
>>> development.
>>> > Does anyone know what would be involved in doing something like this or
>>> > perhaps what files would need to be edited?
>>> >
>>> >
>>> > ___
>>> > 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"
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>>>
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>>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>
> ___
> Please keep all replies on the list by using "reply all"
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___
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[galaxy-dev] Fwd: New galaxy parameter type

2016-07-15 Thread Martin Čech 
forwarding to the list


-- Forwarded message -
From: Katherine Beaulieu 
Date: Fri, Jul 15, 2016 at 3:45 PM
Subject: Re: [galaxy-dev] New galaxy parameter type
To: Martin Čech 


Thanks Peter, I will look into that. The reason I am asking is because of
what Mohammed asked earlier as well. I developed two tools which allow you
to import and export information from a program called irods but you need
to be able to authenticate with irods to be able to do so. Thanks again for
always being helpful!

On Fri, Jul 15, 2016 at 3:10 PM, Martin Čech  wrote:

> Katherine please disregard my answer, I probably misread your question. :)
> M.
>
> On Fri, Jul 15, 2016 at 3:05 PM Peter Cock 
> wrote:
>
>> Did you mean parameter as in input field shown
>> to the user? Like a combobox or text field?
>>
>> Since this happened to come up earlier today, here's
>> a rejected pull request which added a password
>> parameter - that ought to give you a rough idea:
>>
>> https://github.com/galaxyproject/galaxy/pull/393
>>
>> Peter
>>
>> On Fri, Jul 15, 2016 at 7:46 PM, Katherine Beaulieu
>>  wrote:
>> > Hi everyone,
>> > I am looking to implement a new parameter type for galaxy tool
>> development.
>> > Does anyone know what would be involved in doing something like this or
>> > perhaps what files would need to be edited?
>> >
>> >
>> > ___
>> > 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/
>
>
___
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/