Implement a tool for migrating raw bioassays to derived bioassays

[Nicklas Nordborg]

Future development of BASE may remove things that are not used much anymore. For example, raw bioassays with raw data imported into the database, experiments, array lims, etc.

We have a lot of data at the raw bioassay level but they are also a bit problematic since it is a dead end in the sense that it is not possible to create more child items for other analysis. Until now it has been solved by adding more files and/or annotations to an existing raw bioassay.

It would be a lot more flexible if we could move existing raw bioassays to the derived bioassay level instead. In theory it could be done with batch importers, but in practice it would be better to implement a tool for that.

The general idea is to create a derived bioassay copy of each raw bioassay. The platform/variant/rawdatatype are used to map to a subtype. Existing annotations, files, any-to-any links, etc. are re-linked to the new derived bioassays (they will no longer be available on the raw bioassay).

Below is more detailed description (not yet complete):

Database columns

RawBioAssays	DerivedBioAssays	Comment
id	id	A new ID is generated
version	version	Copy
diskusage_id	-	Not used
annotationset_id	annotationset_id	Copy and clear
fileset_id	fileset_id	Copy and clear
entry_date	entry_date	Copy
platform_id variant_id rawdatatype	subtype_id	Platform and rawdata type is mapped to a subtype
job_id	job_id	Copy
protocol_id	protocol_id	Copy
software_id	software_id	Copy
arraydesign_id	-	Create an AnyToAny-link
bioassay_id	-	Link via ParentDerivedBioassays and ParentPhysicalBioAssays
extract_id	extract_id	Copy
name	name	Copy
description	description	Copy
removed_by	removed_by	Copy
itemkey_id	itemkey_id	Copy
projectkey_id	projectkey_id	Copy
owner	owner	Copy
has_data	-	Not used
spots	-	Not used
file_spots	-	Not used
bytes	-	Not used
-	is_root	false
-	kit_id	null
-	hardware_id	null