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
On Tue, Jan 20, 2015 at 2:45 PM, Dooley, Damion <Damion.Dooley(a)bccdc.ca>
I was successful getting library dataset selection and form
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....
#for $i, $dataset in enumerate($library_datasets)
Successfully submits either the full file path of selected dataset, or its
However trying to rerun this history tool item gets us an error (not
related to the above <command> contents):
View as: Interactive | Text | XML (full)
⇝ AttributeError: 'int' object has no attribute 'id'
Module galaxy.tools.parameters.basic:146 in value_to_basic
>> return self.to_string( value, app )
Module galaxy.tools.parameters.basic:2406 in to_string
app <galaxy.app.UniverseApplication object at 0x59a0710>
object at 0x7fced01d2090>
>> 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 [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
Input Parameter Value Note for rerun
BLAST results as XML 240: megablast Pasted Entry vs
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:
var link = $(this);
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