Commit 44256971 authored by mvdbeek's avatar mvdbeek
Browse files

Fix ColumnSetAction post job action 

If columns are specified as integers this would fail currently.
Reported by Peter Briggs on the [mailing list](https://lists.galaxyproject.org/archives/list/galaxy-dev@lists.galaxyproject.org/thread/PXLCVKIZ5LW3MLI6333PFMANYGOCDLD2/)
parent 177a2a1c

lib/galaxy/jobs/actions/post.py

+4 −3
Original line number Diff line number Diff line
@@ -277,6 +277,7 @@ class ColumnSetAction(DefaultJobAction): 
                for k, v in action.action_arguments.items():

                    if v:

                        # Try to use both pure integer and 'cX' format.

                        if not isinstance(v, int):

                            if v[0] == 'c':

                                v = v[1:]

                            v = int(v)

lib/galaxy/workflow/modules.py

+2 −1
Original line number Diff line number Diff line
@@ -40,6 +40,7 @@ from galaxy.tools.parameters.basic import ( 
    workflow_building_modes

)

from galaxy.tools.parameters.wrapped import make_dict_copy

from galaxy.util import unicodify

from galaxy.util.bunch import Bunch

from galaxy.util.json import safe_loads

from galaxy.util.odict import odict
@@ -1124,7 +1125,7 @@ class ToolModule(WorkflowModule): 
        replacement_parameters = set()

        for pja in step.post_job_actions:

            for argument in pja.action_arguments.values():

                for match in re.findall(r'\$\{(.+?)\}', argument):

                for match in re.findall(r'\$\{(.+?)\}', unicodify(argument)):

                    replacement_parameters.add(match)



        return list(replacement_parameters)