Register destruction of stored samples and extracts in the "Retraction wizard"

[Nicklas Nordborg]

The typical situation is that a "Retract" or "RetroNo" is received and registered some time after samples has been received and processed. In this case, the protocol for finding and destroying samples stored in the freezers will include all existing samples and everything will be good.

However, there is a non-zero probability that a sample is somewhere in the lab waiting to be processed or under processing. In this case the destruction protocol is probably incorrect and/or incomplete. For example, samples may be stored at a temporary location and newly created items may not have been registered yet. If more items are registered after the destruction protocol has been created there is a risk that they are never destroyed.

It is not possible to prevent this situation so the retraction wizard should be improved with more checks to prevent that samples are left in the freezers.

• When the destruction protocol is returned from the lab we need a way to check and register that individual items has been destroyed.
• The final destruction wizard that actually delete things from the database must check that all stored items have been registered as destroyed.
• We need a way to create new destruction protocols at any time that include information about all items that have not yet been destroyed. The protocol may include information about destroyed items also if that is clearly marked.

[Nicklas Nordborg]

In 5637:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

Enabled the RetractStatus annotation for samples and extracts and added Destroyed value to it.

The "Destruct" functionality will check that all Specimen, Lysate, RNA, DNA and FlowThrough items have this annotation set before allowing items to be deleted.

The idea is that the "Edit" functionality that is currently used for registering dates also should be used to set RetractStatus=Destroyed on the above items.

[Nicklas Nordborg]

In 5638:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

Added a link to create a protocol in the Retraction follow-up wizard.

The protocol itself need to be redesigned because it currently requires the number of items as a parameter and we don't have that number in the follow-up wizard.

[Nicklas Nordborg]

In 5639:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

Re-designed the protocol to not require the number of items to destroy beforehand. It is now also possible to submit a "patientId" instead of a "caseName".

[Nicklas Nordborg]

In 5640:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

Added "BloodDNA" subtype to list of types that should be explicitely checked for destruction.

[Nicklas Nordborg]

In 5641:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

Fixed parameter name on URL for loading the protocol.

[Nicklas Nordborg]

In 5642:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

The lab protocol now indicates which items that have already been registered as destroyed.

[Nicklas Nordborg]

In 5643:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

Added a list of items that need to marked as destroyed to the "Edit" dialog. All items must be checked for the status to be changed to ReadyForDestruction.

[Nicklas Nordborg]

In 5644:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

Create an event setting the remaining quantity to 0 when an item is marked as destroyed.

[Nicklas Nordborg]

In 5646:

References #1188: Register destruction of stored samples and extracts in the "Retraction wizard"

Re-ordered columns in the retraction follow-up wizard to make it easier to click on the correct action for a specific patient.