Dynamic Tool UI based on script

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Dynamic Tool UI based on script

evan clark
Is it possible to execute a script within a tool xml confit to retrieve some data and append to the ui depending on the requested data. I.e if I wanted to get a list of files and provide them as select options before hitting the execute button.


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Re: Dynamic Tool UI based on script

E. Rasche
Hi Evan,

Yes, it is possible. Please note that these will not/may not work in
workflows as expected and the use of code files is generally
discouraged. (That said, in some cases you care more about user
experience than anything else, and here they are useful.)

Here's an example from my Apollo tool suite which lets the user interact
with a service that lives outside of Galaxy. The user is able to select
from a dropdown which dataset they would like to retrieve from that
system (filtering on ones that they have permissions for.)

Here I define an input with a dynamic_options parameter:
https://github.com/galaxy-genome-annotation/galaxy-tools/blob/master/tools/apollo/macros.xml#L62

I specify at the top of my tool which code file I want to load:
https://github.com/galaxy-genome-annotation/galaxy-tools/blob/master/tools/apollo/fetch_organism_jbrowse.xml#L8

Now when this is accessed, it looks at the code file paramater and calls
the appropriate function: (There's a bit of unrelated stuff going on in
here to handle caching since those calls are called many times and my
backend is slow)
https://github.com/galaxy-genome-annotation/galaxy-tools/blob/master/tools/apollo/webapollo.py#L1578

Eventually this is called whcih shows the expected return format:
https://github.com/galaxy-genome-annotation/galaxy-tools/blob/master/tools/apollo/webapollo.py#L1524
A list of tuples where the first parameter is what the user sees, the
second parameter is what value the option has (that is passed on the
command line), and the third is "False".

Cheers,

On 2017-11-23, Evan Clark wrote:
> Is it possible to execute a script within a tool xml confit to retrieve some data and append to the ui depending on the requested data. I.e if I wanted to get a list of files and provide them as select options before hitting the execute button.  
>
> --- Sent from VMware Boxer
>

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Re: Dynamic Tool UI based on script

Hans-Rudolf Hotz
In reply to this post by evan clark
Hi Evan

Yes, this is possible with "dynamic_options"

e.g.:

<tool ...

<inputs>

<param name="year" type="select" label="from which year"
      display="radio" refresh_on_change="true" >
               <option value="/2017" selected="true">2017</option>
              <option value="/2016">2016</option>
               <option value="/2015">2015</option>
         </param>

<param name="file" type="select" label="select a run"
     display="radio"
     dynamic_options="ds_readFiles(year)"/>


</inputs>
<outputs>
...
</outputs>
<help>
...
</help>
<code file="more_code.py" />

</tool>

The python function "ds_readFiles" is defined in a extra code file
"more_code.py", which is stored in the same directory as the tool
definition file. The function returns all files with a matching file
name (i.e.year), and could look like:


rDir = "/data/"

def ds_readFiles(year):

     l = os.listdir(rDir)
     p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
     l.sort()
     path = rDir
     filesoptions = [(s) for s in l if os.path.exists(path + s)]
     files = [(s,s,False) for s in filesoptions if p.match(s)]
     return files



a similar case is also described here:

http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html


Hope this helps, Hans-Rudolf


On 11/23/2017 06:02 PM, Evan Clark wrote:

> Is it possible to execute a script within a tool xml confit to retrieve
> some data and append to the ui depending on the requested data. I.e if I
> wanted to get a list of files and provide them as select options before
> hitting the execute button.
>
>
> ---
> Sent from VMware Boxer
>
>
> ___________________________________________________________
> 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/
>
___________________________________________________________
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Re: Dynamic Tool UI based on script

Steve Cassidy
Hi all, 
  this would help in a tool I’m trying to write too but the problem I have implementing this approach is that my script will need an external python module - is there any way that I can list dependencies for the script?  As it happens these are the same dependancies that the tool itself will need once executed.

Thanks,

Steve

Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz <[hidden email]> wrote:

Hi Evan

Yes, this is possible with "dynamic_options"

e.g.:

<tool ...

<inputs>

<param name="year" type="select" label="from which year"
    display="radio" refresh_on_change="true" >
             <option value="/2017" selected="true">2017</option>
     <option value="/2016">2016</option>
             <option value="/2015">2015</option>
</param>

<param name="file" type="select" label="select a run"
   display="radio"
   dynamic_options="ds_readFiles(year)"/>


</inputs>
<outputs>
...
</outputs>
<help>
...
</help>
<code file="more_code.py" />

</tool>

The python function "ds_readFiles" is defined in a extra code file
"more_code.py", which is stored in the same directory as the tool definition file. The function returns all files with a matching file name (i.e.year), and could look like:


rDir = "/data/"

def ds_readFiles(year):

   l = os.listdir(rDir)
   p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
   l.sort()
   path = rDir
   filesoptions = [(s) for s in l if os.path.exists(path + s)]
   files = [(s,s,False) for s in filesoptions if p.match(s)]
   return files



a similar case is also described here:

http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html


Hope this helps, Hans-Rudolf


On 11/23/2017 06:02 PM, Evan Clark wrote:
Is it possible to execute a script within a tool xml confit to retrieve
some data and append to the ui depending on the requested data. I.e if I
wanted to get a list of files and provide them as select options before
hitting the execute button.


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Re: Dynamic Tool UI based on script

Hans-Rudolf Hotz
Hi Steve

what happened, when you add this module to the environment the galaxy
server is running in? (e.g. by listing the path in the 'run.sh' file)

Regards, Hans-Rudolf


On 12/07/2017 03:05 AM, Steve Cassidy wrote:

> Hi all,
>    this would help in a tool I’m trying to write too but the problem I
> have implementing this approach is that my script will need an external
> python module - is there any way that I can list dependencies for the
> script?  As it happens these are the same dependancies that the tool
> itself will need once executed.
>
> Thanks,
>
> Steve
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
>> On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> Hi Evan
>>
>> Yes, this is possible with "dynamic_options"
>>
>> e.g.:
>>
>> <tool ...
>>
>> <inputs>
>>
>> <param name="year" type="select" label="from which year"
>>     display="radio" refresh_on_change="true" >
>>              <option value="/2017" selected="true">2017</option>
>>      <option value="/2016">2016</option>
>>              <option value="/2015">2015</option>
>> </param>
>>
>> <param name="file" type="select" label="select a run"
>>    display="radio"
>>    dynamic_options="ds_readFiles(year)"/>
>>
>>
>> </inputs>
>> <outputs>
>> ...
>> </outputs>
>> <help>
>> ...
>> </help>
>> <code file="more_code.py" />
>>
>> </tool>
>>
>> The python function "ds_readFiles" is defined in a extra code file
>> "more_code.py", which is stored in the same directory as the tool
>> definition file. The function returns all files with a matching file
>> name (i.e.year), and could look like:
>>
>>
>> rDir = "/data/"
>>
>> def ds_readFiles(year):
>>
>>    l = os.listdir(rDir)
>>    p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
>>    l.sort()
>>    path = rDir
>>    filesoptions = [(s) for s in l if os.path.exists(path + s)]
>>    files = [(s,s,False) for s in filesoptions if p.match(s)]
>>    return files
>>
>>
>>
>> a similar case is also described here:
>>
>> http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html
>>
>>
>> Hope this helps, Hans-Rudolf
>>
>>
>> On 11/23/2017 06:02 PM, Evan Clark wrote:
>>> Is it possible to execute a script within a tool xml confit to retrieve
>>> some data and append to the ui depending on the requested data. I.e if I
>>> wanted to get a list of files and provide them as select options before
>>> hitting the execute button.
>>>
>>>
>>> ---
>>> Sent from VMware Boxer
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>>>
>> ___________________________________________________________
>> 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/
>
___________________________________________________________
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:
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Re: Dynamic Tool UI based on script

Steve Cassidy
I could do that but it would mean that no-one could install the tool from the toolshed without also installing this package. 

Maybe I just need to hack this together.

Steve


Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 7 Dec 2017, at 6:59 pm, Hans-Rudolf Hotz <[hidden email]> wrote:

Hi Steve

what happened, when you add this module to the environment the galaxy server is running in? (e.g. by listing the path in the 'run.sh' file)

Regards, Hans-Rudolf


On 12/07/2017 03:05 AM, Steve Cassidy wrote:
Hi all,
  this would help in a tool I’m trying to write too but the problem I
have implementing this approach is that my script will need an external
python module - is there any way that I can list dependencies for the
script?  As it happens these are the same dependancies that the tool
itself will need once executed.

Thanks,

Steve


Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz <[hidden email]
<mailto:[hidden email]>> wrote:

Hi Evan

Yes, this is possible with "dynamic_options"

e.g.:

<tool ...

<inputs>

<param name="year" type="select" label="from which year"
   display="radio" refresh_on_change="true" >
            <option value="/2017" selected="true">2017</option>
    <option value="/2016">2016</option>
            <option value="/2015">2015</option>
</param>

<param name="file" type="select" label="select a run"
  display="radio"
  dynamic_options="ds_readFiles(year)"/>


</inputs>
<outputs>
...
</outputs>
<help>
...
</help>
<code file="more_code.py" />

</tool>

The python function "ds_readFiles" is defined in a extra code file
"more_code.py", which is stored in the same directory as the tool
definition file. The function returns all files with a matching file
name (i.e.year), and could look like:


rDir = "/data/"

def ds_readFiles(year):

  l = os.listdir(rDir)
  p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
  l.sort()
  path = rDir
  filesoptions = [(s) for s in l if os.path.exists(path + s)]
  files = [(s,s,False) for s in filesoptions if p.match(s)]
  return files



a similar case is also described here:

http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html


Hope this helps, Hans-Rudolf


On 11/23/2017 06:02 PM, Evan Clark wrote:
Is it possible to execute a script within a tool xml confit to retrieve
some data and append to the ui depending on the requested data. I.e if I
wanted to get a list of files and provide them as select options before
hitting the execute button.


---
Sent from VMware Boxer


___________________________________________________________
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/

___________________________________________________________
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and other Galaxy lists, please use the interface at:
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___________________________________________________________
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Re: Dynamic Tool UI based on script

Hans-Rudolf Hotz

Sure

However, tools relying on "dynamic_options" and extra "code" scripts are
usually 'hacks' for accessing external data/services in a local galaxy
installation. And such tools are not intended for the toolshed
anyway....IMHO.


Hans-Rudolf


On 12/07/2017 09:37 AM, Steve Cassidy wrote:

> I could do that but it would mean that no-one could install the tool
> from the toolshed without also installing this package.
>
> Maybe I just need to hack this together.
>
> Steve
>
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
>> On 7 Dec 2017, at 6:59 pm, Hans-Rudolf Hotz <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>> Hi Steve
>>
>> what happened, when you add this module to the environment the galaxy
>> server is running in? (e.g. by listing the path in the 'run.sh' file)
>>
>> Regards, Hans-Rudolf
>>
>>
>> On 12/07/2017 03:05 AM, Steve Cassidy wrote:
>>> Hi all,
>>>   this would help in a tool I’m trying to write too but the problem I
>>> have implementing this approach is that my script will need an external
>>> python module - is there any way that I can list dependencies for the
>>> script?  As it happens these are the same dependancies that the tool
>>> itself will need once executed.
>>>
>>> Thanks,
>>>
>>> Steve
>>>
>>> —
>>> Department of Computing, Macquarie University
>>> http://web.science.mq.edu.au/~cassidy
>>>
>>>> On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz <[hidden email]
>>>> <mailto:[hidden email]>> wrote:
>>>>
>>>> Hi Evan
>>>>
>>>> Yes, this is possible with "dynamic_options"
>>>>
>>>> e.g.:
>>>>
>>>> <tool ...
>>>>
>>>> <inputs>
>>>>
>>>> <param name="year" type="select" label="from which year"
>>>>    display="radio" refresh_on_change="true" >
>>>>             <option value="/2017" selected="true">2017</option>
>>>>     <option value="/2016">2016</option>
>>>>             <option value="/2015">2015</option>
>>>> </param>
>>>>
>>>> <param name="file" type="select" label="select a run"
>>>>   display="radio"
>>>>   dynamic_options="ds_readFiles(year)"/>
>>>>
>>>>
>>>> </inputs>
>>>> <outputs>
>>>> ...
>>>> </outputs>
>>>> <help>
>>>> ...
>>>> </help>
>>>> <code file="more_code.py" />
>>>>
>>>> </tool>
>>>>
>>>> The python function "ds_readFiles" is defined in a extra code file
>>>> "more_code.py", which is stored in the same directory as the tool
>>>> definition file. The function returns all files with a matching file
>>>> name (i.e.year), and could look like:
>>>>
>>>>
>>>> rDir = "/data/"
>>>>
>>>> def ds_readFiles(year):
>>>>
>>>>   l = os.listdir(rDir)
>>>>   p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
>>>>   l.sort()
>>>>   path = rDir
>>>>   filesoptions = [(s) for s in l if os.path.exists(path + s)]
>>>>   files = [(s,s,False) for s in filesoptions if p.match(s)]
>>>>   return files
>>>>
>>>>
>>>>
>>>> a similar case is also described here:
>>>>
>>>> http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html
>>>>
>>>>
>>>> Hope this helps, Hans-Rudolf
>>>>
>>>>
>>>> On 11/23/2017 06:02 PM, Evan Clark wrote:
>>>>> Is it possible to execute a script within a tool xml confit to retrieve
>>>>> some data and append to the ui depending on the requested data. I.e
>>>>> if I
>>>>> wanted to get a list of files and provide them as select options before
>>>>> hitting the execute button.
>>>>>
>>>>>
>>>>> ---
>>>>> Sent from VMware Boxer
>>>>>
>>>>>
>>>>> ___________________________________________________________
>>>>> 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/
>>>>>
>>>> ___________________________________________________________
>>>> 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/
>>>
>
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: Dynamic Tool UI based on script

Steve Cassidy
 I don’t like ‘hacks’!! I solved this by pulling the relevant bits of the module into my script so that it runs with no dependencies. It’s basically just making an HTTP GET request with an authentication header, so not too hard to achieve.  Should be safe to put in the toolshed.

Thanks, this is a big improvement in our UI (and I vote for not deprecating this feature, maybe even making it more robust).

Steve

Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 7 Dec 2017, at 8:50 pm, Hans-Rudolf Hotz <[hidden email]> wrote:


Sure

However, tools relying on "dynamic_options" and extra "code" scripts are usually 'hacks' for accessing external data/services in a local galaxy installation. And such tools are not intended for the toolshed anyway....IMHO.


Hans-Rudolf


On 12/07/2017 09:37 AM, Steve Cassidy wrote:
I could do that but it would mean that no-one could install the tool
from the toolshed without also installing this package.

Maybe I just need to hack this together.

Steve



Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 7 Dec 2017, at 6:59 pm, Hans-Rudolf Hotz <[hidden email]
<[hidden email]>> wrote:

Hi Steve

what happened, when you add this module to the environment the galaxy
server is running in? (e.g. by listing the path in the 'run.sh' file)

Regards, Hans-Rudolf


On 12/07/2017 03:05 AM, Steve Cassidy wrote:
Hi all,
 this would help in a tool I’m trying to write too but the problem I
have implementing this approach is that my script will need an external
python module - is there any way that I can list dependencies for the
script?  As it happens these are the same dependancies that the tool
itself will need once executed.

Thanks,

Steve


Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz <[hidden email]
<mailto:[hidden email]>> wrote:

Hi Evan

Yes, this is possible with "dynamic_options"

e.g.:

<tool ...

<inputs>

<param name="year" type="select" label="from which year"
  display="radio" refresh_on_change="true" >
           <option value="/2017" selected="true">2017</option>
   <option value="/2016">2016</option>
           <option value="/2015">2015</option>
</param>

<param name="file" type="select" label="select a run"
 display="radio"
 dynamic_options="ds_readFiles(year)"/>


</inputs>
<outputs>
...
</outputs>
<help>
...
</help>
<code file="more_code.py" />

</tool>

The python function "ds_readFiles" is defined in a extra code file
"more_code.py", which is stored in the same directory as the tool
definition file. The function returns all files with a matching file
name (i.e.year), and could look like:


rDir = "/data/"

def ds_readFiles(year):

 l = os.listdir(rDir)
 p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
 l.sort()
 path = rDir
 filesoptions = [(s) for s in l if os.path.exists(path + s)]
 files = [(s,s,False) for s in filesoptions if p.match(s)]
 return files



a similar case is also described here:

http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html


Hope this helps, Hans-Rudolf


On 11/23/2017 06:02 PM, Evan Clark wrote:
Is it possible to execute a script within a tool xml confit to retrieve
some data and append to the ui depending on the requested data. I.e
if I
wanted to get a list of files and provide them as select options before
hitting the execute button.


---
Sent from VMware Boxer


___________________________________________________________
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/

___________________________________________________________
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/


___________________________________________________________
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:
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