Convert all raw bioassay items to derived bioassays

[Nicklas Nordborg]

The raw bioassay level is problematic since it doesn't allow us to create child items. Since we no longer use any raw bioassay specific features it would be a lot nicer to have everything at the derived bioassay level. Downstream analysis can then be added as child items instead of just adding more files and annotations to existing items.

This is a huge work that require a lot of changes to existing wizards.

We also need a way to convert existing raw bioassays to derived bioassays without losing any information. We might need some help of low-level BASE functionality here. See ​https://base.thep.lu.se/ticket/2321

Data releases and the Relax server is also affected.

[Nicklas Nordborg]

In 7682:

References #1581: Convert all raw bioassay items to derived bioassays

Marking RawBioAssay-related things in Reggie (and also in the BASE code) as deprecated. We get 1136 compilation warnings.

[Nicklas Nordborg]

In 7706:

References #1581: Convert all raw bioassay items to derived bioassays

Added 3 new subtypes that are replacement for raw data types:

• GeneExpression: Used for Cufflinks and StringTie raw bioassays
• VariantCall: Used for Variant call raw bioassays
• OncoArray: Used for the OncoArray500K raw bioassays

Item list and file type definitions have been updated to use derived bioassays instead of raw bioassays.

Note that the changes here will cause the installation wizard to display a lot of errors since normally the item type used by an item list or file type can't be modified. Before updating to this version the BASE tool for converting raw bioassays to derived bioassays should be used. The following mapping must be used:

• cufflinks raw data type must be mapped to GeneExpression.
• variant.sequencing.stringtie raw data type must be mapped to GeneExpression, and the gene.tsv files that use the Generic raw data file type must be changed to FPKM file type.
• variant.sequencing.variant-call must be mapped to VariantCall.
• variant.genotyping.oncoarray500K must be mapped to OncoArray.

[Nicklas Nordborg]

In 7707:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed the "Case summary" so that it load the new derived bioassay items. This also includes a slightly different fix for #1590.

[Nicklas Nordborg]

In 7708:

References #1581: Convert all raw bioassay items to derived bioassays

The SSP plugin and related wizard has been updated. Auto-confirmation integration remains since StringTie and reports have not yet been updated.

[Nicklas Nordborg]

In 7709:

References #1581: Convert all raw bioassay items to derived bioassays

The StringTie pipeline has been updated.

[Nicklas Nordborg]

In 7710:

References #1581: Convert all raw bioassay items to derived bioassays

The Legacy pipeline has been updated.

[Nicklas Nordborg]

In 7711:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed all reports.

[Nicklas Nordborg]

In 7712:

References #1581: Convert all raw bioassay items to derived bioassays

Counters for reports.

[Nicklas Nordborg]

In 7713:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for the StringTie/2023 pipeline.

[Nicklas Nordborg]

In 7714:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for the Yellow label wizard.

[Nicklas Nordborg]

In 7715:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for Flagged RNA wizard.

[Nicklas Nordborg]

In 7716:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for the variant calling and targeted genotyping pipelines.

[Nicklas Nordborg]

In 7717:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for the WGS variant calling pipeline.

[Nicklas Nordborg]

In 7718:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for stray folder and secondary analysis cleanup wizards.

[Nicklas Nordborg]

In 7719:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for the thumbnails and VCF file links that can appear in table listings and other places.

[Nicklas Nordborg]

In 7720:

References #1581: Convert all raw bioassay items to derived bioassays

Found some more things related to thumbnails.

[Nicklas Nordborg]

In 7721:

References #1581: Convert all raw bioassay items to derived bioassays

Removed RAWBIOASSAY from all annotation types.

[Nicklas Nordborg]

In 7722:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for imputation and PRS wizards.

[Nicklas Nordborg]

In 7723:

References #1581: Convert all raw bioassay items to derived bioassays

Fond some more places that used raw bioassays.

[Nicklas Nordborg]

In 7724:

References #1581: Convert all raw bioassay items to derived bioassays

Fixed for the release exporter.

[Nicklas Nordborg]

In 7725:

References #1581: Convert all raw bioassay items to derived bioassays

Cleaning up comments, documentation and fixing some other minor things. Removed rawbioassay-related code that is no longer used.

[Nicklas Nordborg]

In 7730:

References #1581: Convert all raw bioassay items to derived bioassays

More cleaning up.

[Nicklas Nordborg]

Milestone renamed