Opened 10 months ago

Closed 8 months ago

#1209 closed task (fixed)

Add support for storing TMA specimen

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

Description (last modified by Nicklas Nordborg)

TMA are sometimes created by external projects. We want to track some information about this so that we at least can say for which patients a TMA exists and were to find it.

We need to define a few things to be able to store TMA specimen.

A new SAMPLE subtype: TMASpecimen.

  • It should be a child item of Case.
  • The name should be auto-generated as: <case>.tma, <case>.tma2
  • The external/release id should be auto-generated as: T<NNNNNN>

Annotations:

  • TMABlock: Name of the TMA block on which the sample is located.
  • TMABlockPos: Position on the block. In some coordinate system that at least can be understood by the person responsible for the external project.
  • PAD: The PAD that was used as source for the TMA. Typically it should match a PAD of a specimen/no-specimen, but it may also be different.
  • PADRequested: The PAD that was originally requested. This should always match a PAD of an existing specimen/no-specimen.
  • SampleOwner: Name of the external project/person that is responsible for the TMA.
  • More ???

An import wizard for importing TMA data should also be created. It should be able to read from an text or Excel file. It will need a way to identify the case. The simplest solution would be to have the name of the case in the file. But it would also be possible to find the correct case by personal number and laterality or maybe by PAD on specimen.

Once a parent case has been found a TMASpecimen can be created and named automatically. Most annotations are taken from columns in the file. The ExternalProject annotation should be the same for all, so this can be an input parameter in the import wizard.

Change History (11)

comment:1 Changed 10 months ago by Nicklas Nordborg

In 5774:

References #1209: Add support for storing TMA specimen

Added new subtype for TMASpecimen and annotation types TMABlock and TMABlockPos.

comment:2 Changed 10 months ago by Nicklas Nordborg

In 5777:

References #1209: Add support for storing TMA specimen

First version of a TMA importer plug-in. It is very similar to existing batch importers in BASE, but can only be used in "create" mode. So far, the only required column is a case name. If the case exists a new TMASpecimen child item is created. The name and external id of the new item is auto-generated.

comment:3 Changed 10 months ago by Nicklas Nordborg

In 5778:

References #1209: Add support for storing TMA specimen

Implemented support for importing annotations TMABlock, TMABlockPos and PAD.

comment:4 Changed 10 months ago by Nicklas Nordborg

Status: newaccepted

comment:5 Changed 10 months ago by Nicklas Nordborg

In 5779:

References #1209: Add support for storing TMA specimen

Added a "Comment" column which will go into the "description" field of the TMA specimen that are created.

Implemented check for null values in Case name, TMABlock, TMABlockPos and PAD.

comment:6 Changed 10 months ago by Nicklas Nordborg

In 5781:

References #1209: Add support for storing TMA specimen

Added support for using either "Name" or "External ID" to reference existing cases.

comment:7 Changed 10 months ago by Nicklas Nordborg

Description: modified (diff)

comment:8 Changed 10 months ago by Nicklas Nordborg

In 5798:

References #1209: Add support for storing TMA specimen

Added SampleOwner annotation and added this to the TMASpecimenImporter as a job parameter. All TMA samples in a given import will get the same value.

comment:9 Changed 10 months ago by Nicklas Nordborg

In 5799:

References #1209: Add support for storing TMA specimen

Added PADRequested annotation and added this to the TMASpecimenImporter as a job parameter.

comment:10 Changed 9 months ago by Nicklas Nordborg

In 5806:

References #1209: Add support for storing TMA specimen

Display the same options for selection as described in the help text.

comment:11 Changed 8 months ago by Nicklas Nordborg

Resolution: fixed
Status: acceptedclosed
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