GPL-771 Migrate all samples to use the new filtered_positive fields

[Chris-Friend]

User story
In migrating to Beckman, we have added new filtered_positive fields to samples. These simplify the existing "fit to pick" rules distributed throughout various codebases/queries. As such, and before any fit to pick rule changes, we should migrate all old samples to include filtered_positive values in both Mongo and MLWH, and update any queries to simply check the value of the filtered_positive field.

This will also mean we only have to change the fit to pick rules in one place: crawler, where the fields are first set on inserting/updating samples.

Who are the primary contacts for this story
Katy T
Eduardo M
Phil
Chris F

Acceptance criteria
To be considered successful the solution must allow:

• Migrate all samples as per the "Migration to apply pickable decision (crawler)" in this diagram: get all samples from mongo -> apply the filtered positive rules in crawler to them -> update mongo -> update MLWH. It may be possible to do this by simplifying the crawler migration implemented as part of GPL-733.
• Change the STAGE_MATCH_POSITIVE and POSITIVE_SAMPLES_MONGODB_FILTER to use the new filtered_positive field: a sample is fit to pick if this is True See https://github.com/sanger/General-Backlog-Items/issues/80
• Update any queries used by/sent to PaM to instead use the new filtered_positive field See GPL-718 Update PAM report querys to reflect changes in design General-Backlog-Items#81

Additional context
Add any other context or screenshots about the feature request here.

[rl15]

From March 2020 to 17th Dec migration = 17H