Add Kit item

[Nicklas Nordborg]

A Kit is an item that should represent a kit/collection of reagents and other stuff used in the lab to do something.

To begin with we intend to keep the Kit item as simple as possible. For example we do not add special data structures for keeping track of individual items in a kit (use annotations for that).

A kit should have:

• Name and description (implement the Nameable interface).
• Registration date (implement the Registered interface).
• Access is controlled via regular project/user/group sharing (implement the Ownable/Shareable interfaces)
• A subtype so we can filter kits to be used at a specific step in the lab process (implement the Subtypable interface)
• An inactive flag that indicates if the kit can still be used or not.
• An expirationDate for storing the recommended last date the kit should be used.

Selecting inactive kits or using kits after the expiration date should not be forbidden in the core API. It should be used by applications to make sensible default selections.

Kits are linked from:

• Biomaterial events (samples, extracts, physical bioassays)
• Bioplate events
• Derived bioassays (since the first derived bioassay typically represents the sequencing of a flow cell)
• More??

Besides the usual list/view/edit pages in the web client we need to implement and update some other things:

• A batch item importer for kits
• The annotation importer should support kits
• Add kits to the "Item overview" and some new validation rules:
  • Check the expiration date against the creation date of items that has used the kit
• Add kits to "Item subtypes"
• Inherit annotations from kits
• More??

[Nicklas Nordborg]

(In [6989]) References #1958: Add Kit item

Added KitData item in the data layer and links to it from the BioMaterialEventData and BioPlateEventData classes.

Increasing the database schema version.

[Nicklas Nordborg]

(In [6990]) References #1958: Add Kit item

Added Kit item in the core layer and links to it from the BioMaterialEvent and BioPlateEvent classes.

Added TestKit for testing the kit item.

[Nicklas Nordborg]

(In [6991]) References #1958: Add Kit item

Added interface to the web client for listing, viewing and editing kits.

[Nicklas Nordborg]

(In [6992]) References #1958: Add Kit item

Kits can now be selected for extracts in the web client.

Subtype relationships has been implemented and the installer creates "Extraction", "Labeling" and "Library preparation" kit types linked to "Extract", "Labeled extract" and "Library" item types.

[Nicklas Nordborg]

(In [6993]) References #1958: Add Kit item

Kits can now be selected for samples and other events in the web client.

[Nicklas Nordborg]

(In [6994]) References #1958: Add Kit item

Kits can now be selected for physical bioassays.

[Nicklas Nordborg]

(In [6995]) References #1958: Add Kit item

Update recently used kits when the item subtype is changed.

[Nicklas Nordborg]

(In [6996]) References #1958: Add Kit item

Kits can now be selected for derived bioassays.

[Nicklas Nordborg]

(In [6997]) References #1958: Add Kit item

Kits can now be selected for bioplate events.

[Nicklas Nordborg]

(In [6998]) References #1958: Add Kit item

Implemented a Kit batch importer plug-in and added support for setting Kit in other batch importers:

• Derived bioassay importer
• Extract Importer
• Physical bioassay importer
• Sample importer

[Nicklas Nordborg]

(In [7003]) References #1960 and #1958: Inherit annotations from Hardware, Software and Protocol

Fixed in the items listed and added Kit:s to the list of items to inherit from.

[Nicklas Nordborg]

(In [7004]) References #1958: Add Kit item

Added KitLoader that load kit items in the "Item overview". The kit loader is called from the other loaders that have items linking to a kit (bioplate, derived bioassay, extract, physical bioassay and sample).

[Nicklas Nordborg]

(In [7005]) References #1958: Add Kit item

Added KitValidator for validating kit items in the "Item overview".

[Nicklas Nordborg]

(In [7006]) References #1958: Add Kit item

Added extension points for the kit toolbars and edit dialog.

[Nicklas Nordborg]

(In [7041]) References #1958: Add Kit item

The 'roles' test should ingore warnings about missing kits since it doesn't create or use kits.

[Nicklas Nordborg]

(In [7044]) References #1958: Add Kit item

"Kit" was not visible in the view/edit role web pages so it was not possible to assign permissions to other roles that what was set as default (Power user=CREATE).