Assign new labels for samples with legacy labels that need an incremented nucleic acid counter

[ao508]

What if an ALT ID has multiple sample type abbreviations, even in the legacy data?

In the event that a sample with a given ALT ID has multiple sample type abbreviations associated with it but they're all under the general "tumor" umbrella then resolve the sample type to T
However, if an ALT ID has a mix of tumor type sample type abbreviations and the data coming in is resolving to something like N (or L, U - basically anything that isn't a tumor) then this should be flagged and not get a label generated. (Maybe this is something we can include in the validation report to indicate why a sample wasn't assigned a label even though the metadata is technically correct?)

For samples with legacy labels that are duplicate (the same as other IGO sample IDs), should these samples get new labels with incremented nucleic acid counts?

YES. We want to make corrections to sample labels to increment the nucleic acid counter (ex: sample that was IMPACT seq'd and then WES seq'd, even if their legacy labels are identical, we want them to have diff nucleic acid counters)

2. Can we set igoComplete to true for samples that have it as false if that's the only thing preventing it from getting a label generated in SMILE, at least for these samples with legacy labels that need corrections.

SMILE will temporarily override these values and set them to igoComplete=true to force the label generator to make a new label for these samples. Voyager will be notified ahead of time to ignore sample updates. Once all label updates are finished running, SMILE will revert igoComplete=false.

Work required for this: modify the existing script that identifies samples needing an updated/corrected label and publish sample data as an update to SMILE

[ao508]

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