Unverified Commit ce400589 authored by Martin Cech's avatar Martin Cech Committed by GitHub
Browse files

Merge pull request #14908 from mvdbeek/backport_data_column_fix 

[21.09] Backport 14518: Always call strip() on data_column column values
parents e3d05618 a01c8c5a

lib/galaxy/tools/parameters/basic.py

+8 −2
Original line number Diff line number Diff line
@@ -1259,6 +1259,11 @@ class ColumnListParameter(SelectToolParameter): 
        self.is_dynamic = True

        self.usecolnames = input_source.get_bool("use_header_names", False)



    def to_json(self, value, app, use_security):

        if isinstance(value, str):

            return value.strip()

        return value



    def from_json(self, value, trans, other_values=None):

        """

        Label convention prepends column number with a 'c', but tool uses the integer. This
@@ -1292,8 +1297,9 @@ class ColumnListParameter(SelectToolParameter): 
    @staticmethod

    def _strip_c(column):

        if isinstance(column, str):

            if column.startswith('c') and len(column) > 1 and all(c.isdigit() for c in column[1:]):

                column = column.strip().lower()[1:]

            column = column.strip()

            if column.startswith("c") and len(column) > 1 and all(c.isdigit() for c in column[1:]):

                column = column.lower()[1:]

        return column



    def get_column_list(self, trans, other_values):

lib/galaxy_test/api/test_workflows.py

+29 −1
Original line number Diff line number Diff line
@@ -1319,7 +1319,35 @@ steps: 
      col_names: 'B'

""", history_id=history_id)



    @skip_without_tool('column_param')

    @skip_without_tool("column_param_list")

    def test_comma_separated_columns_with_trailing_newline(self):

        # Tests that workflows with weird tool state continue to run.

        # In this case the newline may have been added by the workflow editor

        # text field that is used for data_column parameters

        with self.dataset_populator.test_history() as history_id:

            job_summary = self._run_jobs(

                """class: GalaxyWorkflow

steps:

  empty_output:

    tool_id: empty_output

    outputs:

      out_file1:

        change_datatype: tabular

  column_param_list:

    tool_id: column_param_list

    in:

      input1: empty_output/out_file1

    state:

      col: '2,3\n'

      col_names: 'B\n'

""",

                history_id=history_id,

            )

            job = self.dataset_populator.get_job_details(job_summary.jobs[0]["id"], full=True).json()

            assert "col 2,3" in job["command_line"]

            assert 'echo "col_names B" >>' in job["command_line"]



    @skip_without_tool("column_param")

    def test_runtime_data_column_parameter(self):

        with self.dataset_populator.test_history() as history_id:

            self._run_jobs("""class: GalaxyWorkflow