Opened 4 years ago

Closed 4 years ago

#1214 closed task (fixed)

Add support for external specimen

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.25
Component: net.sf.basedb.reggie Keywords:


This would be similar to the current support for external RNA items that can be created (manually or with the wizard #1187), but instead we start out with a Specimen item that should go into the regular 'Partition wizard'. The assumption is that the specimen is received in RNALater.

The approach is to try and see what happens to existing wizards. The minimal required information is that the specimen should have a name with a short prefix prefix (that are not digits) followed by an underscore and then some custom name. It is recommended that the name is short so that the name including suffixes added to child items can fit on regular labels. 9-10 characters (including the prefix should probably work).

To begin with the registration is manual or done with regular batch item importers.

  • It should be possible to register new external items without them showing up in any wizard to begin with. This may require that the AutoProcessing annotation is set to Disable.
  • Changing the AutoProcessing annotation to ReProcess (or some other value if needed) should make the external item to appear for selection in the "Partition wizard". The handling is similar to "Paused specimen" so it can probably appear in the selection list together with them. The external specimen should be included in the "Pick list", and they should be included in the generated "Label file". A new box position should be generated and the new positions can be in the regular SCAN-B boxes (eg. SpNNN).
  • DNA/RNA extraction should follow the normal procedure
  • RNA Normalization should follow the normal procedure
  • RNAQC should follow the normal procedure
  • After extraction the external RNA should be "paused" again and NOT automatically included in the library preparation. This can probably be done by setting AutoProcessing to Disabled.
  • It should be possible to manually add the RNA to a new mRNA plate just as external RNA is currently handled. After that the library preparation, sequencing and secondary analysis should follow the normal procedure.

Change History (7)

comment:1 by Nicklas Nordborg, 4 years ago

In 5782:

References #1214: Add support for external specimen

Changes to partition wizard to make it more compatible with external specimen. It now possible to register external specimen without a box and location. The sorting in the partition form has been fixed so that specimen without a box are sorted last by name (the default is to sort by box location). However, this would conflict with the sorting required to get "paused" and "re-extract" specimen correct in the second step so there is a re-sorting to put external specimen together with paused specimen in that step.

It was also noticed that registration of external specimen will affect counters on the front page and maybe also the statistics produced by the sample count reports and sample processing statistics. Since the external specimen can't be assigned to a site they are never grouped with site-specific data, but they may still be included in totals. This need to be checked but is not part of ticket.

comment:2 by Nicklas Nordborg, 4 years ago

Status: newaccepted

comment:3 by Nicklas Nordborg, 4 years ago

In 5783:

References #1214: Add support for external specimen

Display "External specimen" in the remark column.

comment:4 by Nicklas Nordborg, 4 years ago

In 5784:

References #1214: Add support for external specimen

Histology images for external specimen got an incorrect folder location (eg. /home/SCANB/HistologyImagesNN_External.his.he1/). The code has been fixed to place external histology images in /home/External/HistologyImages/NN/ where NN is the prefix before the first underscore in the specimen name.

comment:5 by Nicklas Nordborg, 4 years ago

In 5785:

References #1214: Add support for external specimen

When an external specimen has been extracted either the RNA or the pre-normalized RNA is marked with AutoProcessing=Disable since the library preparation of external RNA should always be a manual action.

The DNA from external specimen are by default NOT pre-normalized since a pre-normalized DNA always get a specific location on the next MIPs plate.

If DNA from external specimen should go into the MIPs pipeline they can be selected for pre-normalization at a later time.

comment:6 by Nicklas Nordborg, 4 years ago

In 5786:

References #1214: Add support for external specimen

Fixes an issue with generating the secondary analysis top-level folder for external specimen. The old code stopped at the lysate level since it was only considering EXTRACT items. It now moves all the way up to the specimen item and the name of the specimen now becomes the name of the top-level folder.

It seems like all other wizards are working as expected.

comment:7 by Nicklas Nordborg, 4 years ago

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