convert_to_stringlist: Convert a delimited string to a stringlist annotation

In nf-osi/nfportalutils: NF Portal Utilities

Convert a delimited string to a stringlist annotation

Description

This is a schema change operation that updates 1) column type to list and 2) sets a new ⁠max string length⁠ parameter of a Synapse Table (usually shrinking the max value). It can optionally consult a metadata model about a good ⁠max string length⁠. (and might handle ⁠max list length⁠ in the future if that could be encoded in the model as well). When a model is consulted, as a built-in check an error will be thrown if the data model doesn't recognize the key being changed, i.e. when one wants to be strict about a key in the Table not documented by the model. When there is no model to involve (schema = NULL), the ⁠max string length⁠ will simply be set based on the current values after processing the delimited list (the original code).

Usage

convert_to_stringlist(
  fileview_id,
  annotation_key,
  sep = ",",
  trim_ws = TRUE,
  schema = NULL,
  dry_run = TRUE
)

Arguments

fileview_id	The synapse id of a fileview. Must have the desired annotations in the schema, and must have the files to annotate included in the scope. Must have write access to the files you want to re-annotate.
annotation_key	A character string of the annotation to switch from a delimited string to a stringlist.
sep	The delimiter in the character string. Default = ",".
trim_ws	Remove white space at the beginning and end of list items (e.g. "NF1, NF2" and "NF1,NF2" will yield the same STRING_LIST result). Default = TRUE.
schema	Optional, path to a readable .jsonld schema to use for setting new col schema. See details.
dry_run	Skip upload to table and instead prints study tibble. Default = TRUE.

Value

If dry_run == T, returns list of updates and skips upload.

nf-osi/nfportalutils documentation built on Feb. 26, 2024, 1:05 p.m.