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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