Opened 6 years ago

Closed 6 years ago

#740 closed task (fixed)

Add support for reprocessing specimen

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v3.2
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

It should be possible to reprocess specimen items that has already been processed once. This should be initialized by the Flagged RNA reprocessing wizard (#455) by setting AutoProcessing=ReProcess on the specimen item.

The reprocessing starts at the partition wizard which should get two selection lists. One for the normal flow and one list for the items to reprocess. If items are selected from the reprocessing list it should be possible to generate a protocol with a pick list so that the specimen tubes can be found in the freezer.

The second step in the wizard need some changes:

  • It should be clearly noted which specimen are being reprocessed and which are from the regular flow (important if mixing).
  • It should be possible to take a histology piece for all items, but it is usually not done for reprocessed items and the histology weight should default to 0.
  • The OperatorPartionComment and NofPieces annotations should be displayed but not be modifiable.
  • New positions should be generated for the reprocessed items since it has a number of advantages:
    • It will be easier to put everything in the freezer again in just one box.
    • Downstream wizards which simply generate positions for other items (eg. Lysate, DNA, RNA, etc.) can continue to work as before.

Change History (14)

comment:1 Changed 6 years ago by Nicklas Nordborg

Description: modified (diff)

comment:2 Changed 6 years ago by Nicklas Nordborg

Status: newassigned

comment:3 Changed 6 years ago by Nicklas Nordborg

(In [3144]) References #740: Add support for reprocessing specimen

Adds counter on the index page that include specimen tubes marked with AutoProcessing=ReProcess.

Install servlet adds AutoProcessing annotation to Specimen item type.

comment:4 Changed 6 years ago by Nicklas Nordborg

(In [3145]) References #740: Add support for reprocessing specimen

Started to redesign the partition wizard.

The first step now contains two lists. One for specimen from normal flow and one for specimen to be re-extracted. A pick list can (and should) be printed if specimen are selected from the second list.

The second step has been modified so that specimen for re-extraction has it's own section. The fields for Bloody/Apperance?/etc. has been replaced with the OperatorPartitionComment annotation. The weight and number of pieces are also displayed.

Registration does not work. Label file generation does not work. New box positions are not generated.

comment:5 Changed 6 years ago by Nicklas Nordborg

(In [3146]) References #740: Add support for reprocessing specimen

Label generation now counts existing child items (for histology and lysates) and generate a label file with proper suffixes.

'.l' suffix is now also include in labels for RNA, DNA and flowthrough.

No label is created for the specimen tube when re-exctracting and a histology label is an extra option that must be manually selected.

comment:6 Changed 6 years ago by Nicklas Nordborg

(In [3147]) References #740: Add support for reprocessing specimen

Comparing weight measurements of re-extracted specimen with the current remaining quantity. In theory they should sum up to the same value and we display a warning if the difference is larger than 2 mg.

comment:7 Changed 6 years ago by Nicklas Nordborg

(In [3149]) References #740: Add support for reprocessing specimen

Loading new positions for re-extraction specimen. We use the same method/servlet as in the specimen registration wizard and display them in the partition table form.

Since the positions can't be reservered we need to verify them just before registration. They WILL be taken by other specimen if another user is working with the 'specimen tube registration wizard' at the same time. If the positions has changed during the partitioning they are updated with new positions and the user is notified and asked to confirm before registration.

comment:8 Changed 6 years ago by Nicklas Nordborg

(In [3150]) References #740: Add support for reprocessing specimen

Registration of re-extraction is now possible.

  • The specimen will be moved to now box positions
  • AutoProcessing annotation is reset
  • OperatorPartitionComment and NofPieces are not set
  • A new Lysate (and optionally a Histology item) are created and properly named with index number
  • If the new weight measurements differ more than 1mg from the current remaining quantity an event is added to correct for the difference

comment:9 Changed 6 years ago by Nicklas Nordborg

(In [3151]) References #740: Add support for reprocessing specimen

Some minor adjustments to make the gui easier to use when re-extracting:

  • Histology weight start out as valid (=0)
  • Auto-focus move from ApWeight to SpWeight (skipping HisWeight)

Added utility method to display storage box location.

comment:10 Changed 6 years ago by Nicklas Nordborg

(In [3153]) References #740: Add support for reprocessing specimen

Adjustments to checking the selection of specimen. A warning is displayed if selecting specimen for re-extraction without also selecting all regular specimen.

comment:11 Changed 6 years ago by Nicklas Nordborg

(In [3155]) References #740: Add support for reprocessing specimen

Gray background color in header on the pick list protocol.

comment:12 Changed 6 years ago by Nicklas Nordborg

(In [3160]) References #740: Add support for reprocessing specimen

Typo.

comment:13 Changed 6 years ago by Nicklas Nordborg

(In [3170]) References #740: Add support for reprocessing specimen

Limit width of OperatorPartitionComment column in case the comment is very long for specimen that are re-extract. This casused the input fields to end up off screen with no scrollbar on the page to access them.

comment:14 Changed 6 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
Note: See TracTickets for help on using tickets.