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Fix rendering of subworkflow steps for workflow testing report#1200

Merged
mvdbeek merged 2 commits intogalaxyproject:masterfrom
simonbray:wf-report-sw-fix
Nov 3, 2021
Merged

Fix rendering of subworkflow steps for workflow testing report#1200
mvdbeek merged 2 commits intogalaxyproject:masterfrom
simonbray:wf-report-sw-fix

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@simonbray
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I have been trying to run tests for a workflow containing a subworkflow and although tests were completing successfully, rendering of the HTML report was failing with:

Traceback (most recent call last):
  File "/home/simon/GitRepos/.planemo/bin/planemo", line 8, in <module>
    sys.exit(planemo())
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/click/core.py", line 1128, in __call__
    return self.main(*args, **kwargs)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/click/core.py", line 1053, in main
    rv = self.invoke(ctx)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/click/decorators.py", line 84, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/cli.py", line 98, in handle_blended_options
    return f(*args, **kwds)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/commands/cmd_test_reports.py", line 32, in cli
    handle_reports(ctx, test_data.structured_data, kwds)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/galaxy/test/actions.py", line 184, in handle_reports
    raise exceptions[0]
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/galaxy/test/actions.py", line 177, in handle_reports
    _handle_test_output_file(
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/galaxy/test/actions.py", line 204, in _handle_test_output_file
    contents = build_report.build_report(
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/reports/build_report.py", line 24, in build_report
    markdown = template_data(environment, 'report_markdown.tpl')
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/reports/build_report.py", line 49, in template_data
    return template.render(**environment)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/jinja2/environment.py", line 1304, in render
    self.environment.handle_exception()
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/reports/report_markdown.tpl", line 78, in top-level template code
    {{render_steps(test.data.invocation_details.values(), display_job_attributes)}}
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/jinja2/runtime.py", line 828, in _invoke
    rv = self._func(*arguments)
  File "/home/simon/GitRepos/.planemo/lib/python3.8/site-packages/planemo/reports/macros.tmpl", line 5, in template
    - **Step {{step_data.order_index + 1}}: {{step_data.workflow_step_label or (step_data.jobs[0].tool_id if step_data.jobs[0] else 'Unlabelled step')|replace("_", "\_")}}**:
jinja2.exceptions.UndefinedError: 'dict object' has no attribute 'order_index'

This change fixed it for me.

@simonbray simonbray requested a review from mvdbeek November 2, 2021 16:50
@mvdbeek
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mvdbeek commented Nov 3, 2021

Thanks for cleaning this up!

@mvdbeek mvdbeek merged commit 247095d into galaxyproject:master Nov 3, 2021
@simonbray simonbray deleted the wf-report-sw-fix branch November 3, 2021 13:44
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2 participants