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SeqWare / seqware

This is the SeqWare Project's main repo.
http://seqware.io/
GNU General Public License v3.0
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SEQWARE-1959 - annotation in workflows #289

Closed denis-yuen closed 9 years ago

denis-yuen commented 9 years ago

This branch name ended up being a total misnomer. While reviewing code, I discovered a slightly broken mechanism for annotations in the GCR and provision files.

I repaired it and hooked it up to the Java API. Note that this totally kicks the can down the curb as far as improving provision files and gcr, but this handles the pressing need for annotations in workflows.

The workflow gives examples of annotating processing events corresponding to jobs and annotating processing events corresponding to provision file events.

morgantaschuk commented 9 years ago

Neat!

It looks like we just have to set sqwfile.getProcessingAccessions().put("key","value), and it annotates the processing event and not the file itself. Is that the desired behaviour forever? I can see when you refactor it in X months time that we might want to annotate the file itself instead of the processing event, and then I can subsequently see writing statements like "if annotation is on processing OR annotation is on file" forever.

denis-yuen commented 9 years ago

@morgantaschuk As you probably guessed, I called it "getProcessingAnnotations" because "getAnnotations" would more logically correspond to annotations on the file itself and would be an obvious next candidate for implementation.

I'll see what I discover tomorrow. The interaction between (Module)Runner and ProvisionFiles looks awful, but we'll see how far I get without giving into my urge to rip everything out and re-factor it.