removal of warning due to updatable inputs feature

[mr-c]

unrecognized extension field `http://commonwl.org/cwltool#generation`.  Did you include a $schemas section?

Very cool feature, but no need to print this warning

Presumably related to #317

[kapilkd13]

Hi @mr-c I am looking at this issue. This arises because here https://github.com/common-workflow-language/cwltool/blob/master/cwltool/draft2tool.py#L540 we are setting generation in the datum, and later validating the schema in line 547 In validation step this generation field is checked if it is present in expected_scheme here and as it is not present in scheme it throws this warning.
I can think of two ways to solve this:

1. somehow add the generation field to the expected_scheme, so that it goes for validation and passes.
2. Add generation field to datum after validation is done so that this field never go for validation.
   I tested second method and its working fine. Should we go with second method?

[mr-c]

Let's try number 2, also we should filter it out of the output object

[kapilkd13]

@mr-c do you mean it should not be present in output like here

[jolb rev] completed success
[joyb rev] {
    "output": {
        "checksum": "sha1$97fe1b50b4582cebc7d853796ebd62e3e163aa3f", 
        "basename": "output.txt", 
        "nameext": ".txt", 
        "nameroot": "output", 
        "http://commonwl.org/cwltool#generation": 0, 
        "location": "file:///C:/users/kapilk%7E1/appdata/local/temp/tmpygovsh/output.txt", 
        "class": "File", 
        "size": 1111
    }
}

I asked this because the reason we are having this warning is that we are adding generation field while collecting output. In this case solution would simply be to avoid setting generation by removing these 2 lines here https://github.com/common-workflow-language/cwltool/blob/master/cwltool/draft2tool.py#L540
Should we do this.

[mr-c]

It should be removed from the final output object, the intermediate ones are fine for now.