Arvados

I think this is actually the same bug as was reported again in #19678, the having a input parameter named name runs into trouble.

Having an input parameter with an id of 'name' does work as long as the type is "string" - the problem occurs when the type is anything other than "string".

Note also that this does not only apply to input parameters but to field names as well.

i.e. this is valid:

'''
type:
type: record
fields:
- name: name
type: string
'''

but this is rejected:
'''
type:
type: record
fields:
- name: name
type: boolean
'''

We have confirmed that simply removing the two places in schema_salad where it explicitly throws a ValidationException when it finds a value for a name field that is not of type str solves this problem, and arvados-cwl-runner still works for all of our test cases. We have not yet investigated why this problem appears to be specific to arvados-cwl-runner and is not an issue for cwltool. That seems a bit surprising since they both use schema_salad, but perhaps they are invoking it in a different way?

Hey Josh! Good to hear from you.

The way that arvados-cwl-runner reads the workflow, packs it, and re-reads the packed version has occasionally turned up bugs on the second trip through the sausage machine (parsing and loading). I'll give this a look.

19678-job-loader @ e2267bd99209651c61425f335230e515421b2ef4

• Fix for parameters called 'name'

• Also fix regression involving default file references appearing in
  nested processes (inline declaration of a tool within a workflow).

• Also fixed some dependency issues preventing arvados/jobs developer
  image from working.

developer-run-tests: #3347

This LGTM, thanks.