#1187 closed task (fixed)

Implement an "External RNA import" wizard

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.24
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

Should be similar to the MIPs DNA importer, but a lot simpler. We need different columns. Required columns would be:

  • Name of RNA (with or without prefix)
  • Storage box name
  • Box row and column

It should be possible to add to existing plates/boxes on empty locations. It should be limited to 9x9 storage boxes to begin with since there is no current implementation that allows on-the-fly changes of the dimensions.

Optional columns:

  • External id
  • Concentration
  • Volume or quantity
  • RNAQC (RIN or RQS)
  • Comment

Change History (9)

comment:1 Changed 14 months ago by Nicklas Nordborg

Status: newaccepted

comment:2 Changed 14 months ago by Nicklas Nordborg

In 5630:

References #1187: Implement an "External RNA import" wizard

Added importer implementation for importing external RNA items. It is very similar to the MIPs aliquot importer but there are a few differences:

  • It requires 9x9 storage boxes
  • It allows adding items to existing boxes if there are empty positions
  • Data columns will be different (but so far only name and plate location have been implemented)
  • There is no check for differences among samples in the same column

comment:3 Changed 14 months ago by Nicklas Nordborg

In 5631:

References #1187: Implement an "External RNA import" wizard

Added wizard for importing external RNA. It is available for users with the LibraryPlateDesigner role.

The wizard seems to be functional, but is still lacking features for importing more data columns.

comment:4 Changed 14 months ago by Nicklas Nordborg

In 5632:

References #1187: Implement an "External RNA import" wizard

Added support for more data columns:

  • Quantity
  • NDConc
  • ND260by230
  • ND260by280
  • RIN
  • RQS


All columns are optional, but if they exists they should contain valid numeric values (or be empty). The Quantity value is saved as the "Original quantity" and must be given in µg. The other values are saved to their corresponding annotations. NDConc must be given in ng/µl.

comment:5 Changed 14 months ago by Nicklas Nordborg

In 5633:

References #1187: Implement an "External RNA import" wizard

Implemented function for showing already occupied locations on existing storage boxes.

comment:6 Changed 14 months ago by Nicklas Nordborg

In 5634:

References #1187: Implement an "External RNA import" wizard

Added activity log entry for the RNA importer.

comment:7 Changed 14 months ago by Nicklas Nordborg

In 5635:

References #1187: Implement an "External RNA import" wizard

Display different information and messages depending on if a storage box already eixsts or not.

comment:8 Changed 14 months ago by Nicklas Nordborg

In 5636:

References #1187: Implement an "External RNA import" wizard

Added warning messages to aliquots without a 'NDConc' or 'Quantity' value. The warning is only added if the columns exists.

comment:9 Changed 13 months ago by Nicklas Nordborg

Resolution: fixed
Status: acceptedclosed
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