I’ve finally had a chance to update the wiki - I’ve updated the
following section to include information about the “dynamic_options=…” option for
populating the select list:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cparam.3E_...
I’ve included the information from this email as an additional example in this section:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coptions.3...
I hope this helps others use this approach or something similar.
Greg Von Kuster
> On Oct 2, 2015, at 12:41 PM, Björn Grüning <bjoern.gruening(a)gmail.com> wrote:
>
> Thanks Greg for this nice example, I guess this is useful for others as
> well!
> I will try to put it into the Wiki soon.
>
> Am 30.09.2015 um 20:05 schrieb Greg Von Kuster:
>> Here’s the answer to my question:
>>
>> The ability to use associated dynamic select lists on Galaxy tool forms where
selecting an option in the first select list dynamically re-renders the options in the
second select list is possible after this change:
>>
>>
https://github.com/galaxyproject/galaxy/pull/815
<
https://github.com/galaxyproject/galaxy/pull/815>
>>
>> In my case, I am populating both dynamic select lists from metadata elements
associated with my tool’s single input dataset. The 2 metadata elements I’m using look
like this.
>>
>> MetadataElement( name="field_names", default=[], desc="Field
names",
>> readonly=True, optional=True,
>> visible=True, no_value=[] )
>> # The keys in the field_components map to the list of field_names in the
above element
>> # which ensures order for select list options that are built from it.
>> MetadataElement( name="field_components", default={},
desc="Field names and components",
>> readonly=True, optional=True, visible=True, no_value={} )
>>
>>
>> My tool config includes a code file tag like this.
>>
>> <code file="tool_form_utils.py" />
>>
>>
>> Here are the relevant input parameters in my tool config. The first parameter is
the input dataset that includes the above metadata elements.
>>
>>
>> <param name="input" type="data"
format="vtkascii,vtkbinary" label="Shape with uncolored surface
field">
>> <validator type="expression" message="Shape must
have an uncolored surface field.">value is not None and
len(value.metadata.field_names) > 0</validator>
>> </param>
>>
>>
>> The following parameter dynamically renders a select list consisting of the
elements in the “field_names” metadata element associated with the selected input
dataset.
>>
>>
>> <param name="field_name" type="select"
label="Field name" refresh_on_change="True">
>> <options>
>> <filter type="data_meta" ref="input"
key="field_names"/>
>> <validator type="no_options" message="The
selected shape has no uncolored surface fields." />
>> </options>
>> </param>
>>
>>
>> The following parameter calls the “get_field_components_options() method in the
“tool_form_utils.py” code file discussed above. This method returns the value of the input
dataset’s “field_components” metadata element dictionary whose key is the currently
selected “field_name” from the select list parameter above.
>>
>>
>> <param name="field_component_index" type="select"
label="Field component index"
dynamic_options="get_field_components_options(input, field_name=field_name)"
help="Color will be applied to the selected field's component associated with
this index." />
>>
>>
>> Changing the selected option in the “field_name” select list will dynamically
re-render the options available in the associated “field_component_index” select list,
which is the behavior we want.
>>
>>
>> The “get_field_components_options() method looks like this.
>>
>> def get_field_components_options( dataset, field_name ):
>> options = []
>> if dataset.metadata is None:
>> return options
>> if not hasattr( dataset.metadata, 'field_names' ):
>> return options
>> if dataset.metadata.field_names is None:
>> return options
>> if field_name is None:
>> # The expression validator that helps populate the select list of input
>> # datsets in the icqsol_color_surface_field tool does not filter out
>> # datasets with no field field_names, so we need this check.
>> if len( dataset.metadata.field_names ) == 0:
>> return options
>> field_name = dataset.metadata.field_names[0]
>> field_components = dataset.metadata.field_components.get( field_name, [] )
>> for i, field_component in enumerate( field_components ):
>> options.append( ( field_component, field_component, i == 0 ) )
>> return options
>>
>>
>> Greg Von Kuster
>>
>>
>>> On Sep 20, 2015, at 9:51 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
>>>
>>> Hello all,
>>>
>>> I’m working on adding support to the Galaxy framework for datatypes in the
constructive solid geometry (CSG) space and I have several working Galaxy tools and a
visualization plugin that deal with 3d shapes in this environment. All of this work will
soon be contributed to open source.
>>>
>>> For one of the tools, I need to provide 2 select lists on the tool form that
are associated in such a way that when an option in select list 1 is chosen, the options
in select list 2 are altered and re-rendered. This behavior would probably use a
combination of dynamic options and refresh_on_change between the 2 associated select
lists.
>>>
>>> I’ve not seen a tool that does this precisely, so I’m hoping that if it is
currently possible to do this within Galaxy tools, someone will point me to an example.
>>>
>>> If it is not currently possible, I will contribute a PR for supporting it,
but would like some input as to how it should be done.
>>>
>>> Dynamic options are currently rendered using 4 approaches; from_file,
from_dataset, from_parameter and from_data_table. One or more of several filters can then
be applied to the options to alter them if desired.
>>>
>>> Since these CSG tools involve new datatypes, I have flexibility into how the
metadata elements are set up that are needed to render these 2 select lists. A dictionary
may work where the metadata element contents look like this:
>>>
>>> {a: [‘1’, ‘2’], b: [‘3’, ‘4’] }
>>>
>>> The options in select list 1 would be ‘a’ and ‘b’. When ‘a’ is selected,
select list 2 would have options ‘1’ and ‘2’, and when ‘b’ is selected, select list 2
would have options ‘3’ and ‘4’.
>>>
>>> To support this approach, perhaps dynamic options could be enhanced to
include a from_dict option. There would be some complxity involved in associating the
lists using refresh_on_change so that select list 2 is refreshed with the correct options
when select list one is changed. I haven’t yet worked out these details.
>>>
>>> Also, using a dictionary will not keep order for the options, so perhaps a
list of tuples would be better?
>>>
>>> [ [ ‘a’, [‘1’, ‘2’]], [‘b’, [‘3’, ‘4’]]]
>>>
>>> Can someone let me know if this is currently possible, and if so, an example
tool that does it? If it’s not possible, does the above approach seem reasonable, or is
there a better way?
>>>
>>> Thanks very much,
>>>
>>> Greg Von Kuster
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>>
>>
>> ___________________________________________________________
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>>
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>>
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