Arvados

Problem¶

A user wrote a pipeline template that used run-command's task.env directive. They accidentally defined task.env outside script_parameters, in the top-level component definition.

The resulting job failed because of the missing environment. Weirder, task.env did appear as a script_parameter in that job, but as a string like "{ \"KEY\": \"value\" }". It's hard to imagine how this behavior helps, and it made the issue more confusing to debug because task.env at least appeared to be in the script_parameters.

Crunch should either add the parameter without stringifying it, or not add the parameter at all.

Fix¶

We believe this is backward compatibility code for older Arvados pipelines.

• Take out this translation code.
• Before creating any jobs, a-r-p-i should check the entire pipeline for unrecognized component fields like this, and report them all as fatal errors to the user, then abort.
• Add test(s) to the CLI test suite for a-r-p-i.