ArraySchema.items does need typeDSL after all

[mr-c]

• wait for ratification of CWL v1.2.1

@tetron I think I was too tired when I tested this before; here is a simpler example!

[mr-c]

Here is the log from running the rests without the fix:

[gw0] linux -- Python 3.9.7 /home/michael/cwltool/env3.9/bin/python3

version = '1_0'

    @pytest.mark.parametrize("version", ["1_0", "1_1", "1_2"])
    def test_array_items_typedsl(version) -> None:
        """Demonstrate that 'type: array, items: SomeType[]' works."""
        err_code, _, stderr = get_main_output(
            [
                get_data(f"tests/wf/nested_typedsl_v{version}.cwl"),
                get_data("tests/wf/nested_typedsl_job.yml"),
            ]
        )
>       assert err_code == 0
E       assert 1 == 0
E         +1
E         -0

tests/test_examples.py:1601: AssertionError
----------------------------------------------------------------------------- Captured log call -----------------------------------------------------------------------------
INFO     cwltool:main.py:973  3.1.20210906152048
INFO     cwltool:load_tool.py:101 Resolved '/home/michael/cwltool/tests/wf/nested_typedsl_v1_0.cwl' to 'file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_0.cwl'
ERROR    cwltool:main.py:1142 Tool definition failed validation:
tests/wf/nested_typedsl_v1_0.cwl:5:1: checking field `inputs`
tests/wf/nested_typedsl_v1_0.cwl:6:3:   checking object `tests/wf/nested_typedsl_v1_0.cwl#cat_in`
tests/wf/nested_typedsl_v1_0.cwl:7:5:     Field `items` references unknown identifier `File[]`,
                                          tried
                                          file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_0.cwl#File[]
                                          checking field `type`
tests/wf/nested_typedsl_v1_0.cwl:9:7:       Field `items` references unknown identifier `File[]`,
                                            tried
                                            file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_0.cwl#File[]
_______________________________________________________________________ test_array_items_typedsl[1_2] _______________________________________________________________________
[gw2] linux -- Python 3.9.7 /home/michael/cwltool/env3.9/bin/python3

version = '1_2'

    @pytest.mark.parametrize("version", ["1_0", "1_1", "1_2"])
    def test_array_items_typedsl(version) -> None:
        """Demonstrate that 'type: array, items: SomeType[]' works."""
        err_code, _, stderr = get_main_output(
            [
                get_data(f"tests/wf/nested_typedsl_v{version}.cwl"),
                get_data("tests/wf/nested_typedsl_job.yml"),
            ]
        )
>       assert err_code == 0
E       assert 1 == 0
E         +1
E         -0

tests/test_examples.py:1601: AssertionError
----------------------------------------------------------------------------- Captured log call -----------------------------------------------------------------------------
INFO     cwltool:main.py:973  3.1.20210906152048
INFO     cwltool:load_tool.py:101 Resolved '/home/michael/cwltool/tests/wf/nested_typedsl_v1_2.cwl' to 'file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_2.cwl'
ERROR    cwltool:main.py:1142 Tool definition failed validation:
tests/wf/nested_typedsl_v1_2.cwl:5:1: checking field `inputs`
tests/wf/nested_typedsl_v1_2.cwl:6:3:   checking object `tests/wf/nested_typedsl_v1_2.cwl#cat_in`
tests/wf/nested_typedsl_v1_2.cwl:7:5:     Field `items` references unknown identifier `File[]`,
                                          tried
                                          file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_2.cwl#File[]
                                          checking field `type`
tests/wf/nested_typedsl_v1_2.cwl:9:7:       Field `items` references unknown identifier `File[]`,
                                            tried
                                            file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_2.cwl#File[]
_______________________________________________________________________ test_array_items_typedsl[1_1] _______________________________________________________________________
[gw1] linux -- Python 3.9.7 /home/michael/cwltool/env3.9/bin/python3

version = '1_1'

    @pytest.mark.parametrize("version", ["1_0", "1_1", "1_2"])
    def test_array_items_typedsl(version) -> None:
        """Demonstrate that 'type: array, items: SomeType[]' works."""
        err_code, _, stderr = get_main_output(
            [
                get_data(f"tests/wf/nested_typedsl_v{version}.cwl"),
                get_data("tests/wf/nested_typedsl_job.yml"),
            ]
        )
>       assert err_code == 0
E       assert 1 == 0
E         +1
E         -0

tests/test_examples.py:1601: AssertionError
----------------------------------------------------------------------------- Captured log call -----------------------------------------------------------------------------
INFO     cwltool:main.py:973  3.1.20210906152048
INFO     cwltool:load_tool.py:101 Resolved '/home/michael/cwltool/tests/wf/nested_typedsl_v1_1.cwl' to 'file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_1.cwl'
ERROR    cwltool:main.py:1142 Tool definition failed validation:
tests/wf/nested_typedsl_v1_1.cwl:5:1: checking field `inputs`
tests/wf/nested_typedsl_v1_1.cwl:6:3:   checking object `tests/wf/nested_typedsl_v1_1.cwl#cat_in`
tests/wf/nested_typedsl_v1_1.cwl:7:5:     Field `items` references unknown identifier `File[]`,
                                          tried
                                          file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_1.cwl#File[]
                                          checking field `type`
tests/wf/nested_typedsl_v1_1.cwl:9:7:       Field `items` references unknown identifier `File[]`,
                                            tried
                                            file:///home/michael/cwltool/tests/wf/nested_typedsl_v1_1.cwl#File[]

[codecov]

Codecov Report

Merging #1515 (bed518b) into main (6af9932) will decrease coverage by 10.99%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##             main    #1515       +/-   ##
===========================================
- Coverage   66.45%   55.46%   -11.00%     
===========================================
  Files          93       47       -46     
  Lines       16541     8294     -8247     
  Branches     4390     2160     -2230     
===========================================
- Hits        10992     4600     -6392     
+ Misses       4401     3147     -1254     
+ Partials     1148      547      -601     

Impacted Files	Coverage Δ
cwltool/utils.py
cwltool/cuda.py
cwltool/builder.py
cwltool/pathmapper.py
cwltool/checker.py
cwltool/job.py
cwltool/cwlviewer.py
cwltool/context.py
cwltool/sandboxjs.py
cwltool/cwlrdf.py
... and 36 more

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