Yellow label highlighting a representative specimen

[Nicklas Nordborg]

A new annotation named YellowLabel for samples of subtype Specimen. It should be a string enum with one allowed value: yellow (more values may be defined in the future).

At some point, one of the available labels on the pathology referral form will be colored yellow (the yellow label).

When registered, a specimen with the yellow label should be annotated as YellowLabel = yellow. The idea is that the pathologist will highlight a biopsy (using the yellow label) to indicate that it is suitable for further analysis with respect to clinically relevant end-points. That is, a yellow label is the pathologists way of ‘requesting’ a clinical report or at least indicating that a report generated for the specimen should be relevant for the breast cancer.

The pathologist will still have the possibility to collect additional tissue samples (specimen) in separate RNAlater tubes marked with individual labels (not yellow). The instructions to the pathologist will go so far as to specify that if it’s deemed that a representative specimen cannot be collected the yellow label should not be used at all. In such a senario, the pathologist will still have the possibility to collect a non-representative specimen, e.g., a node-metastasis or a piece of tumor adjacent tissue or tumor tissue that the pathologists simply does not deem as representative.

Samples registered with regular labels (not yellow) should be not be annotated.

Samples that are already registered will not be ‘retro’ annotated.

This ticket may be divided into subtickets:

• Changes in specimen registration for marking the YellowLabel tube (#827)
• Gui changes in other wizard to highlight the YellowLabel
  • Pathology referral form (#839)
  • Sample processing wizards (#846)
  • Library preparation wizards (#847)
  • Secondary analysis wizards (#856)
  • Case summary (#852)
  • Flagged RNA (#857)
• Track and report YellowLabel separately (#861)

[Nicklas Nordborg]

Renamed the RepresentativeSpecimen annotation to YellowLabel.

[Nicklas Nordborg]

Milestone renamed

[Nicklas Nordborg]

(In [3770]) References #771: Yellow label highlighting a representative specimen

Added class YellowLabelStatistics. It is intended to be used as a cache for information about yellow label specimen that may be expensive or impractical to retreive in real time. The statistics is controlled by the counter service which means that it should be updated at least once every hour.

To begin with it will simply keep the names of all specimen that has been annotated with the YellowLabel annotation. This list is used by the "Reggie" column action to put the yellow-label icon in the "Reggie" column for items that are derived from yellow-label specimen. The icon is for informational purposes only.

[Nicklas Nordborg]

(In [3771]) References #771: Yellow label highlighting a representative specimen

Decorate the "Case summary" toolbar buttons with the yellow-label icon if the item is a descendant to a yellow-label specimen.