Release exporter changes due to Methylation data

[Nicklas Nordborg]

In tickets #1418 and #1419, we added data from Methylation EPIC chips to lorry. A new item chain from DNA was created: DNA -> DNA aliquot -> BeadChip -> Scan -> Methylation. The BeadChip and Scan items are shared with the Oncoarray genotyping pipeline (#1393).

The current release exporter stops at the topmost DNA level. In the database there is typically a single intermediate DNA aliquot before the BeadChip level.

We need to decide which data that should be included in releases and how to represent the item chain in a more condensed way.

[Nicklas Nordborg]

In 7006:

References #1451: Release exporter changes due to Methylation data

Added MethylationWriter implementation. It currently only export name and type of Methylation items and link directly to the DNA parent item. No other annotations or files are exported yet.

[Nicklas Nordborg]

In 7009:

References #1451: Release exporter changes due to Methylation data

A safer implementation for getting the top-most DNA that should be linked with the methylation item.

[Nicklas Nordborg]

In 7010:

References #1451: Release exporter changes due to Methylation data

Added information about the bead array chip used, including id, type and position.

[Nicklas Nordborg]

In 7019:

References #1451: Release exporter changes due to Methylation data

Added scanner and software information to the export.

[Nicklas Nordborg]

In 7020:

References #1451: Release exporter changes due to Methylation data

Added more annotation for the methylation data.