Opened 4 years ago

Closed 4 years ago

#908 closed enhancement (fixed)

Support for re-processing from lysate

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.7
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

There is a recent use case where RNA/DNA extraction failed and there is no backup specimen left for re-processing. There is enough lysate available for a second extraction. This scenario is currently not supported but should be implemented. Several sub-steps are required:

  • A new action in the "Flagged RNA wizard" for marking a Lysate for re-processing. Setting the AutoProcessing flag to ReProcess should be enough.
  • A new wizard for generating a pick list protocol with information such as freezer position for the lysates that have been marked for re-processing. Completing the wizard should move the lysate items to new positions in ExtraLysNNN boxes. The intention is that the RNA/DNA/FlowThrough should be placed in corresponding positions in Extra**** boxes. The AutoProcessing flag may also have to be cleared or set to some other value.
  • The Extra**** boxes should be created manually by an administrator which also assign freezer positions to them.
  • The protocol wizard and the RNA/DNA/FlowThrough registration wizard get a second list if there are lysates that are ready for a second extraction. The logged in user may select lysate from either the regular and/or the extra list up to 12 in total.
  • The lab protocol should include some kind of visual marker that highlights the "old" lysates. If all lysates are "old" the "Lysis" section in the lab protocol is not used and should be disabled.
  • The RNA/DNA/FlowThrough registration wizard should not update the "Lysis" information on the "old" lysates. The "Lysis" section should be skipped/disabled if all lysates are old. The wizard should also make sure that the new RNA/DNA/FlowThrough is placed in their corresponding Extra**** boxes and that they are correctly named (*.r2, *.d2, ...).

Change History (14)

comment:1 Changed 4 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 4 years ago by Nicklas Nordborg

(In [4086]) References #908: Support for re-processing from lysate

Added "Re-extract from lyste" button to the "Flagged RNA" wizard. It is more or less the same action as "Re-extract from specimen", except that the AutoProcessing flag is set on the lysate instead of on the specimen.

comment:3 Changed 4 years ago by Nicklas Nordborg

(In [4087]) References #908: Support for re-processing from lysate

Added "Pick lysate for re-extraction" wizard to the Reggie start page. Added two counters that count the number of lysates to be picked and the ones that have been picked and are ready for re-extraction.

The counter implementation assume that the AutoProcessing flag is set to ReProcess for both counter but that the picking process move the lysate from a Lys** box to an ExtraLys** box.

comment:4 Changed 4 years ago by Nicklas Nordborg

(In [4089]) References #908: Support for re-processing from lysate

Implemented the first part of the lysate pick list wizard. The wizard will display a list of lysates that has been selected for re-exatraction (by setting the AutoProcessing annotation to ReProcess). The user may select any number of lysatates and are then given a printable pick list protocol. Preliminary storage positions in the extra boxes are assigned at the same time (the existing code from the specimen registration has been refactored and moved to StoragePlate). It will not be possible to continue with the wizard until there is enough space in extra boxes for storing the lysate. The wizard will not create new extra boxes automatically since there are no rules for placing them in the freezers.

The final registration step is not yet implemented.

comment:5 Changed 4 years ago by Nicklas Nordborg

(In [4092]) References #908: Support for re-processing from lysate

Implemented the final registration in the "Pick lysate for re-extraction" wizard. The critical change is to put the lysates in the new positions in the ExtraLys*** box.

The action is also registered as a bioplate MOVE event. This makes it possible to add comments to each lysate with information about the old and new positions. So all is not lost if the pick list protocol goes missing.

comment:6 Changed 4 years ago by Nicklas Nordborg

(In [4093]) References #908: Support for re-processing from lysate

The "Lab tracking protocol for Allprep isolation" now include the lysates that have been picked for re-extraction. They are currently included in the same list as the regular lysates. The protocol will display "Re-extract from lysate!" instead of the Allprep weight. If all selected lysates are re-extraction the "Lysis" section is "disabled".

comment:7 Changed 4 years ago by Nicklas Nordborg

(In [4094]) References #908: Support for re-processing from lysate

Started to modify the "DNA/RNA/FlowThrough registration" wizard to support re-extraction from lysate.

  • The lysates are currently displayed in a single list with re-extraction lysats last.
  • In the second step, the "Lysis" section is disabled if all lysates are for re-extraction.
  • In the third step the "Total" column in the "Lysate" section is displaying the remaining quantity.
  • In the edit dialog for setting values that are different from the defaults, all lysis-related fields are disabled when a re-extraction lysate has been selected. Existing comments are loaded and displayed.
  • Lysis-related information is not modified when regisitering

There are still some issues:

  • RNA/DNA/FlowThrough names are not correctly generated. The suffixes are hardcoded and there is not yet any support for generating .r2 suffixes, etc.

comment:8 Changed 4 years ago by Nicklas Nordborg

(In [4095]) References #908: Support for re-processing from lysate

Generate child RNA/DNA/FlowThrough names with correct suffix.

comment:9 Changed 4 years ago by Nicklas Nordborg

(In [4097]) References #908: Support for re-processing from lysate

The "Lab Tracking Protocol for Allprep isolation" now has separate selection lists for lysates in the regular flow and lysates for re-extraction.

Added a function for generating a label generation file for the new RNA, !PreNormalizedRNA, DNA and FlowThrough tubes. Note that this solution doesn't save the new names and that it could potentially mix up names if re-extracting a lysate multiple times before the new RNA/DNA is registered. In practice, this will never happen since the remaining lysate is just enough for one more extraction.

comment:10 Changed 4 years ago by Nicklas Nordborg

(In [4098]) References #908: Support for re-processing from lysate

Moved the "Reserve selected lysates" checkbox back to the bottom since it was a bit strange to have that on top when there is only one selection list (as there will be in most cases).

comment:11 Changed 4 years ago by Nicklas Nordborg

(In [4099]) References #908: Support for re-processing from lysate

The "DNA/RNA/FlowThrough registration" now has separate selection lists for lysates in the regular flow and lysates for re-extraction.

comment:12 Changed 4 years ago by Nicklas Nordborg

(In [4100]) References #908: Support for re-processing from lysate

Reset the ReservedBy annotation so that the lysates selected for re-extraction are not reserved by the same user that happened to do the original extraction.

comment:13 Changed 4 years ago by Nicklas Nordborg

(In [4101]) References #908: Support for re-processing from lysate

Re-enable commit that was disabled due to debugging. Some minor adjustments to the normalization protocol to make room for longer storage box names (ExtraRNA**).

comment:14 Changed 4 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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