Fix 2d output arrays with format tag

[vjaganat90]

The issue is when we print 2d_output arrays which have "format" tag

touch filename.txt
cwltool --cachedir foo output_2D_file_format.cwl

("Error collecting output for parameter 'output_array': output_2D_file_format.cwl:14:3: list indices must
                                                                                        be integers or
                                                                                        slices, not str",
                                                                                        {})

The crux of the issue is aslist function, only promotes scalars to 1d arrays. Arbitrary JS can return an arbitrary json, format handling code needs to handle arbitrary json (not just scalars or 1d arrays which is done through aslist function).

With this fix the output should be something like this

jaganathv2$ touch filename.txt
jaganathv2$ cwltool --cachedir foo output_2D_file_format.cwl
INFO /Users/jaganathv2/mambaforge/envs/cwt/bin/cwltool 3.1.20220628170239.dev281+g57619ffd
INFO Resolved 'output_2D_file_format.cwl' to 'file:///Users/jaganathv2/Code/WIC/cwltool/tests/output_2D_file_format.cwl'
INFO [job output_2D_file_format.cwl] Output of job will be cached in /Users/jaganathv2/Code/WIC/cwltool/tests/foo/585a1a734523fb1e13030642dc26ad4a
INFO [job output_2D_file_format.cwl] /Users/jaganathv2/Code/WIC/cwltool/tests/foo/585a1a734523fb1e13030642dc26ad4a$ true
INFO [job output_2D_file_format.cwl] completed success
{
    "output_array": [
        [
            {
                "class": "File",
                "location": "file:///Users/jaganathv2/Code/WIC/cwltool/tests/filename.txt",
                "format": "file:///Users/jaganathv2/Code/WIC/cwltool/tests/output_2D_file_format.cwl#some_format",
                "basename": "filename.txt",
                "size": 0,
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "path": "/Users/jaganathv2/Code/WIC/cwltool/tests/filename.txt"
            },
            {
                "class": "File",
                "location": "file:///Users/jaganathv2/Code/WIC/cwltool/tests/filename.txt",
                "format": "file:///Users/jaganathv2/Code/WIC/cwltool/tests/output_2D_file_format.cwl#some_format",
                "basename": "filename.txt",
                "size": 0,
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "path": "/Users/jaganathv2/Code/WIC/cwltool/tests/filename.txt"
            }
        ],
        [
            {
                "class": "File",
                "location": "file:///Users/jaganathv2/Code/WIC/cwltool/tests/filename.txt",
                "format": "file:///Users/jaganathv2/Code/WIC/cwltool/tests/output_2D_file_format.cwl#some_format",
                "basename": "filename.txt",
                "size": 0,
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "path": "/Users/jaganathv2/Code/WIC/cwltool/tests/filename.txt"
            },
            {
                "class": "File",
                "location": "file:///Users/jaganathv2/Code/WIC/cwltool/tests/filename.txt",
                "format": "file:///Users/jaganathv2/Code/WIC/cwltool/tests/output_2D_file_format.cwl#some_format",
                "basename": "filename.txt",
                "size": 0,
                "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
                "path": "/Users/jaganathv2/Code/WIC/cwltool/tests/filename.txt"
            }
        ]
    ]
}INFO Final process status is success

[codecov]

Codecov Report

Attention: Patch coverage is 66.66667% with 3 lines in your changes missing coverage. Please review.

Project coverage is 83.84%. Comparing base (71360db) to head (c73137b).

Files	Patch %	Lines
cwltool/command_line_tool.py	66.66%	1 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2010      +/-   ##
==========================================
+ Coverage   82.87%   83.84%   +0.97%     
==========================================
  Files          46       46              
  Lines        8244     8251       +7     
  Branches     2190     2194       +4     
==========================================
+ Hits         6832     6918      +86     
+ Misses        909      854      -55     
+ Partials      503      479      -24     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[mr-c]

That creates a file in the current working directory. If you need to create new files, please use the tmp_path Pytest fixture to get a safe directory to write into

https://github.com/common-workflow-language/cwltool/blob/main/tests/test_examples.py#L1263-L1268

[mr-c]

Thank you @vjaganat90 ! I've made a note to turn your example into a new conformance test for CWL: common-workflow-language/cwl-v1.3#31

[vjaganat90]

@mr-c if the test passes, please have another look.

[mr-c]

Okay, the conformance test errors are due to common-workflow-language/cwltest#216

[mr-c]

This looks good to me; and we should add a version of this as a CWL v1.3 conformance test. Any thoughts @tetron ?

[tetron]

This looks good to me; and we should add a version of this as a CWL v1.3 conformance test. Any thoughts @tetron ?

Yes, I agree, and I wonder if the spec should have say anything about this behavior as well.

[mr-c]

This looks good to me; and we should add a version of this as a CWL v1.3 conformance test. Any thoughts @tetron ?

Yes, I agree, and I wonder if the spec should have say anything about this behavior as well.

Ah, yes, now that I re-read https://www.commonwl.org/v1.2/CommandLineTool.html#CommandInputParameter , it says

format
optional
string | array<string> | Expression
Only valid when type: File or is an array of items: File.

(The quoted text is the same for CWL v1.1 and v1.0)

And yet, the example from this PR is an array of arrays of Files. So maybe this behavior change has to wait for CWL version 1.3?