Peptide and source assignment tables + protein tree viewer in Arborist frontend

[dmx2]

An attempt to standardize the inputs and modify the code so make serve will show the peptide and source assignments generated by the protein tree codebase along with the protein tree itself.

[jamesaoverton]

Good start. The column.tsv also needs to include these tables. The Makefile task for nanobot.db may also need to create headers for these tables.

[dmx2]

Is there a datatype for floats? The assignment score is not an int (natural_number), and I think I will need to use a float for that datatype.

[jamesaoverton]

Datatypes are configurable. We need better docs, but there are some decent examples here, including decimals: https://github.com/ontodev/nanobot.rs/blob/main/examples/penguins/src/schema/datatype.tsv

For numerics data are restricted by the underlying SQL types and their corresponding Rust types. We currently support SQLite and Postgres, which means we are effectively limited to SQLite's short list of types. So VALVE supports four SQL types in the 'SQLite type' and 'PostgreSQL type' columns of datatype.tsv: text, integer, real, and numeric (effectively the union of integer and real). Here's some relevant code: https://github.com/ontodev/valve.rs/blob/main/src/lib.rs#L2395

(Note that we will soon combine 'SQLite type' and 'PostgreSQL type' columns into a single 'SQL type' column.)