Flagged RNA re-processing wizard

[Nicklas Nordborg]

The wizard for selecting RNA to be processed into mRNA (#424) has the ability to flag some RNA items as not usable. Eg. if there is not enough RNA available (at least 1.1µg is needed). The wizard flags such RNA with AutoProcessing=Disabled and Flag annotations and also put them in the 'Flagged RNA' list.

This wizard should start with the items in the 'Flagged RNA' list and help the user to decide what should happen. In this step there are basically 3 outcomes:

1. There is lysate left which can be used to extract additional RNA. If the existing RNA has at least 0.5µg the additional extraction could possibly be pooled with the existing so that the 1.1µg limit is reached.

2. There is no lysate, but a backup piece is available in the freezer. If this piece is big enough it can maybe be partitioned again for a second try.

3. There is no lysate and no backup.

The flagged RNA might be moved to another list depending on which category it falls into. From there it should be possible for the re-processing to use almost the same workflow as for unprocessed items. This is described in other tickets (to be created).

It is important that re-processed items are tracked at all steps so that it is possible to make special decisions when needed. For example:

• Once we have the re-processed RNA we need to make a decision if it should be pooled with the original RNA or not.
• Plate locations may follow different rules for the re-processed items. Eg. the second batch of RNA/DNA/FlowThrough from a lysate will get different coordinates.

[Nicklas Nordborg]

We should start with implementing support for repartitioning from the specimen level (see #740). The workflow could be something like this:

The list of 'Flagged RNA' is presented together with some useful information:

• Flag value
• Original quantity
• Remaining quantity
• Latest RQS/RIN value
• Amount lysate left
• Amount used from specimen to create lysate
• Amount specimen left
• If a Library child item exists
• If a Raw bioassay child item exists
• Link to 'Case summary' (in popup window)
• more??

It should be possible to filter the list based on the values. Eg. if a certain flag is set, if remaining quantity is above/under a specified limit, etc.

A checkbox for each RNA item should be used to select items.

Action buttons should allow the operator apply an action to the selected RNA items:

• Re-extract from specimen:
  • Set AutoProcessing=ReProcess on the parent specimen
  • Remove the RNA from the 'Flagged RNA' list
• Flag specimen:
  • Add parent specimen to 'Flagged Specimen' list
  • Flag the specimen with the same flag as the RNA
  • Remove the RNA from the 'Flagged RNA' list
• Unflag the RNA
  • Remove the flag value from the RNA item
  • Remove the RNA from the 'Flagged RNA' list

More actions may be implemented in the future:

• Restart at lysate level
• Make new RIN/RQS measurement and to see if the current RNA should continue normal processing

[Nicklas Nordborg]

(In [3158]) References #455: Flagged RNA re-processing wizard

Started with this wizard.

• The index page got a new section with re-processing wizards. Currently the SamplePrep role is required to use the wizard.
• The flagged rna wizard lists all members in the flagged rna list
• A simple filter function has been implemented that filters in the browser only
• The "Re-extract from specimen" action has been implemented

[Nicklas Nordborg]

(In [3161]) References #455: Flagged RNA re-processing wizard

Added 'Unflag' action that simple resets the flag on the RNA item and remove it from the list.

[Nicklas Nordborg]

(In [3162]) References #455: Flagged RNA re-processing wizard

Added 'Flagged Specimen' biomaterial list and 'Flag specimen' action in the wizard.

[Nicklas Nordborg]

(In [3163]) References #455: Flagged RNA re-processing wizard

Added PrepCurator role and restricted access to the flagged rna wizard to users with this role.

[Nicklas Nordborg]

(In [3164]) References #455: Flagged RNA re-processing wizard

Added 'Re-process to libraries' action which sets AutoProcessing=ReProcess, clears the flag and remove the RNA items from the "Flagged RNA" list.

[Nicklas Nordborg]

(In [3165]) References #455: Flagged RNA re-processing wizard

Added 'Create biomaterial list' functionality that can be used to create a new biomaterial list of the selected RNA or their specimen.

[Nicklas Nordborg]

(In [3166]) References #455: Flagged RNA re-processing wizard

Cleaning up the code and trying to improve performance a bit by using snapshot manager for loading annotations. Side effect is that some changes are also required in the mRNA servlet (since we don't want to duplicate code for RNAQC loading).