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More fixes for auto-generating workflow tests#1241

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mvdbeek merged 1 commit intogalaxyproject:masterfrom
mvdbeek:workflow_test_init
Jun 2, 2022
Merged

More fixes for auto-generating workflow tests#1241
mvdbeek merged 1 commit intogalaxyproject:masterfrom
mvdbeek:workflow_test_init

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@mvdbeek mvdbeek commented Jun 2, 2022

Fixes the following traceback when running tests:

Traceback (most recent call last):
  File "/Users/mvandenb/miniconda3/bin/planemo", line 33, in <module>
    sys.exit(load_entry_point('planemo', 'console_scripts', 'planemo')())
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
- doc: Test outline for Generic-variation-analysis-reporting
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/Users/mvandenb/src/planemo/planemo/cli.py", line 96, in handle_blended_options
    return f(*args, **kwds)
  File "/Users/mvandenb/src/planemo/planemo/commands/cmd_test.py", line 78, in cli
    return_value = test_runnables(ctx, runnables, original_paths=uris, **kwds)
  File "/Users/mvandenb/src/planemo/planemo/engine/test.py", line 23, in test_runnables
    test_data = engine.test(runnables)
  File "/Users/mvandenb/src/planemo/planemo/engine/interface.py", line 79, in test
    test_case_data = test_case.structured_test_data(run_response)
  File "/Users/mvandenb/src/planemo/planemo/runnable.py", line 361, in structured_test_data
    return run_response.structured_data(self)
  File "/Users/mvandenb/src/planemo/planemo/runnable.py", line 573, in structured_data
    output_problems.extend(test_case._check_output(output_id, output_value, output_test))
  File "/Users/mvandenb/src/planemo/planemo/runnable.py", line 411, in _check_output
    output_test,
  File "/Users/mvandenb/src/planemo/planemo/test/_check_output.py", line 24, in check_output
    return checker(runnable, output_properties, test_properties, **kwds)
  File "/Users/mvandenb/src/planemo/planemo/test/_check_output.py", line 43, in _check_output_collection
    verify_collection(output_def, data_collection, verify_dataset)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 922, in verify_collection
    verify_elements(data_collection["elements"], output_collection_def.element_tests)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 892, in verify_elements
    element_outfile, element_attrib = element_test
ValueError: too many values to unpack (expected 2)

For ease of use I think it makes sense to just always use path in a
separate map, since you can then add additional keys like compare: and
so on.

Fixes the following traceback when running tests:
```
Traceback (most recent call last):
  File "/Users/mvandenb/miniconda3/bin/planemo", line 33, in <module>
    sys.exit(load_entry_point('planemo', 'console_scripts', 'planemo')())
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
- doc: Test outline for Generic-variation-analysis-reporting
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/decorators.py", line 73, in new_func
    return ctx.invoke(f, obj, *args, **kwargs)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/Users/mvandenb/src/planemo/planemo/cli.py", line 96, in handle_blended_options
    return f(*args, **kwds)
  File "/Users/mvandenb/src/planemo/planemo/commands/cmd_test.py", line 78, in cli
    return_value = test_runnables(ctx, runnables, original_paths=uris, **kwds)
  File "/Users/mvandenb/src/planemo/planemo/engine/test.py", line 23, in test_runnables
    test_data = engine.test(runnables)
  File "/Users/mvandenb/src/planemo/planemo/engine/interface.py", line 79, in test
    test_case_data = test_case.structured_test_data(run_response)
  File "/Users/mvandenb/src/planemo/planemo/runnable.py", line 361, in structured_test_data
    return run_response.structured_data(self)
  File "/Users/mvandenb/src/planemo/planemo/runnable.py", line 573, in structured_data
    output_problems.extend(test_case._check_output(output_id, output_value, output_test))
  File "/Users/mvandenb/src/planemo/planemo/runnable.py", line 411, in _check_output
    output_test,
  File "/Users/mvandenb/src/planemo/planemo/test/_check_output.py", line 24, in check_output
    return checker(runnable, output_properties, test_properties, **kwds)
  File "/Users/mvandenb/src/planemo/planemo/test/_check_output.py", line 43, in _check_output_collection
    verify_collection(output_def, data_collection, verify_dataset)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 922, in verify_collection
    verify_elements(data_collection["elements"], output_collection_def.element_tests)
  File "/Users/mvandenb/miniconda3/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 892, in verify_elements
    element_outfile, element_attrib = element_test
ValueError: too many values to unpack (expected 2)
```

For ease of use I think it makes sense to just always use path in a
separate map, since you can then add additional keys like `compare:` and
so on.
@mvdbeek mvdbeek requested a review from simonbray June 2, 2022 14:57
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Thanks for fixing that!

@mvdbeek mvdbeek merged commit 4c8606f into galaxyproject:master Jun 2, 2022
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