Unverified Commit 2699f8c7 authored by mvdbeek's avatar mvdbeek
Browse files

Fix unbound local error in sort collection tool 

Fixes
```
UnboundLocalError: local variable 'sorted_elements' referenced before assignment
  File "galaxy/tools/__init__.py", line 1909, in handle_single_execution
    rval = self.execute(
  File "galaxy/tools/__init__.py", line 2005, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/model_operations.py", line 83, in execute
    self._produce_outputs(
  File "galaxy/tools/actions/model_operations.py", line 108, in _produce_outputs
    tool.produce_outputs(
  File "galaxy/tools/__init__.py", line 3490, in produce_outputs
    for dce in sorted_elements:
```
in https://sentry.galaxyproject.org/share/issue/264aea1fd3994e5ba67ab80fcbd2c577/
parent e7092b6d

lib/galaxy/tools/__init__.py

+2 −2
Original line number Diff line number Diff line
@@ -3408,7 +3408,7 @@ class SortTool(DatabaseOperationTool): 
        sorttype = incoming["sort_type"]["sort_type"]

        new_elements = {}

        elements = hdca.collection.elements

        presort_elements = []

        presort_elements = None

        if sorttype == "alpha":

            presort_elements = [(dce.element_identifier, dce) for dce in elements]

        elif sorttype == "numeric":
@@ -3433,7 +3433,7 @@ class SortTool(DatabaseOperationTool): 
        else:

            raise Exception(f"Unknown sort_type '{sorttype}'")



        if presort_elements:

        if presort_elements is not None:

            sorted_elements = [x[1] for x in sorted(presort_elements, key=lambda x: x[0])]



        for dce in sorted_elements:

lib/galaxy_test/api/test_workflows.py

+37 −0
Original line number Diff line number Diff line
@@ -5155,6 +5155,43 @@ input: 
        put_response = self._update_workflow(workflow_id, workflow_object)

        assert put_response.status_code == 200



    def test_empty_collection_sort(self):

        self._run_workflow(

            """class: GalaxyWorkflow

inputs:

  input: collection

  filter_file: data

steps:

  filter_collection:

    tool_id: __FILTER_FROM_FILE__

    in:

       input: input

       how|filter_source: filter_file

  sort_collection_1:

    tool_id: __SORTLIST__

    in:

      input: filter_collection/output_filtered

  sort_collection_2:

    tool_id: __SORTLIST__

    in:

      input: filter_collection/output_discarded

  merge_collection:

    tool_id: __MERGE_COLLECTION__

    in:

      inputs_0|input: sort_collection_1/output

      inputs_1|input: sort_collection_2/output

test_data:

  input:

    collection_type: list

    elements:

      - identifier: i1

        content: "0"

  filter_file: i1

""",

            wait=True,

            assert_ok=True,

        )



    @skip_without_tool("random_lines1")

    def test_run_replace_params_over_default_delayed(self):

        with self.dataset_populator.test_history() as history_id: