GPL-699 Result 'Limit of detection' == 'Positive' [Heron] [3]

[rl15]

User story
GPL-699 | As Lead Covid-19 Statistical Geneticist (Jeff B) I would like samples with a result of 'Limit of detection' to be treated the same as a positive result in col E of plate map files

Who are the primary contacts for this story
Rich L
Cristina A

Acceptance criteria
To be considered successful the solution must allow:

• On finding value of 'Limit of detection' in result column E change crawler behaviour to see this as positive to be picked, given current Ct rules

Dependencies
Need to clarify if values 'Detected' and 'Not Detected' are Positive and Negative respectively

Additional context
Data is parsed today as result of GPL-654. As of 22nd Oct, no results of 'Limit of detection' have been seen in wild.

[harrietc52]

UPDATE:

• A GPL-654 commit added "limit of detection" to the ALLOWED_RESULT_VALUES in Crawler.
• "limit of detection" now needs to be added to allowed positive values. Note: make sure isn't case senstivie
• There was also a comment TODO: confirm! 'Detected', 'Not detected'?, which has since been removed. Who can clarify if values 'Detected' and 'Not Detected' are Positive and Negative respectively?

[Chris-Friend]

Note if this is required, it breaks the assumption that only RESULT=Positive samples can be fit to pick. This impacts on a few places in the crawler and lighthouse projects that specifically look for/only process RESULT=Positive samples

[rl15]

Tanya B wrote (Friday, 11 December 2020 at 12:49)

[John S ] said they [ assume Milton Keynes - rl15, see ] were having trouble implementing this, hence why we haven’t seen any values coming through. However, it is still required and so can we open it again, but place the story on hold. Not a priority until we have an update.

NB last mail out on this was sent rl15 Wednesday, 9 December 2020 at 17:20

[rl15]

Alan K wrote (Thursday, 15 April 2021 at 14:58)

Having discussed with Sonia and Cristina we are happy to deprecate