Fix handling of missing progression data

[arahuja]

For now pfs and os are just zero-d when not available, though we should have proper na handling.

See hammerlab/cohorts#46

[jburos]

I'm curious why these would ever be NA - the XML version of the clin data has a field last_contact_days_to, for example, which can be used to populate these values. If they are actually unknown, then a value of 0 seems appropriate. Not sure if there an analogous field available from the cases endpoint of the API.

In general seems likely we will want/need a few post-processing steps for clin data.

[arahuja]

I saw a few cases where last_contact_days_to or I think it's called days_to_last_follow_up or something was also None. There was also a case where this was longer than the OS which was odd.

[jburos]

Interesting. I see a field called followup_lost_to which may also be informative?

Perhaps we should look at annotations for these use cases, to see if they can help reconcile the issues.

[hammer]

@jburos what is this blocked on?

[jburos]

@hammer The blocking issue is hammerlab/cohorts#46 (cohorts doesn't currently support unknown progression/mortality status).