Hey Damion,
Thanks a lot for the description. We are currently switching the tool form
to a newer version but I will look into this fix soon and should be able
transfer it.
Thanks,
Sam
On Tue, Jan 20, 2015 at 2:45 PM, Dooley, Damion <damion.doo...@bccdc.ca>
wrote:
> I was successful getting library dataset selection and form submission to
> happen within tool form tool form input <param type="library_data" ...> -
> Yay! But it appears one last fix (besides the "url:
> "/visualization/list_libraries",' bug) is needed to enable history tool
> item to be RERUN.
>
> So if a galaxy dev can tackle this, great! Otherwise I'll have to drop
> this approach :<(
>
> *****************
> For others who may need...
>
> tool form's param:
>
> <param name="library_datasets" type="library_data"
> label="Reference Bin file" help="Select one reference bin at a time from
> the popup window's Reference Bin library."/>
>
> <command> tag contents....
>
> #if $library_datasets
> -B "
> #for $i, $dataset in enumerate($library_datasets)
> #$dataset.get_file_name()
> $dataset.id
> #end for
> "
> #end if
>
> Successfully submits either the full file path of selected dataset, or its
> id.
>
> *****************
> However trying to rerun this history tool item gets us an error (not
> related to the above <command> contents):
>
> Error Traceback:
> View as: Interactive | Text | XML (full)
> ⇝ AttributeError: 'int' object has no attribute 'id'
> ....
> Module galaxy.tools.parameters.basic:146 in value_to_basic
> view
> >> return self.to_string( value, app )
> Module galaxy.tools.parameters.basic:2406 in to_string
> app <galaxy.app.UniverseApplication object at 0x59a0710>
> ldda 331
> self <galaxy.tools.parameters.basic.LibraryDatasetToolParameter
> object at 0x7fced01d2090>
> value [331]
> >> return [ldda.id for ldda in value]
> AttributeError: 'int' object has no attribute 'id'
>
> which is in /lib/galaxy/tools/parameters/basic.py:
>
> class LibraryDatasetToolParameter( ToolParameter ):
> """
> Parameter that lets users select a LDDA from a modal window,
> then use it within the wrapper.
> """
>
> ...
> def to_string( self, value, app ):
> if not value:
> return value
> return [ldda.id for ldda in value]
>
> "Value" is getting an array of dataset ids, whereas this method is
> expecting value to be a list of dataset objects. I tried changing ldda.id
> to just "id" but found other parts of LibraryDatasetTool code were broken
> as they too were expecting an object. Maybe this is related to the tool
> job's history detail link showing "Reference Bin file" as a string label of
> an object?:
>
> Input Parameter Value Note for rerun
> BLAST results as XML 240: megablast Pasted Entry vs
> 16SMicrobial.fasta
> Reference Bin file
> [<galaxy.model.LibraryDatasetDatasetAssociation object at 0x7fcee04d4350>]
> Tabular Report Column Labels Short name
> HTML Report template templates.html_report
>
>
>
> ********************************
> The other bug:
>
> 2) Tool_form.mako has a hardcoded url that doesn't work for galaxy
> installs that have a prefix so that needs adjustment:
>
> $(".add-librarydataset").click(function() {
> var link = $(this);
> $.ajax({
> url: "/visualization/list_libraries",
> ___________________________________________________________
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