update_study_annotations: Updates a set of files with project-level annotations.

In nf-osi/nfportalutils: NF Portal Utilities

Updates a set of files with project-level annotations.

Description

Adds studyId, studyName, initiative, funder annotations to a set of files from a fileview query. Assumes that projectId==studyId. You must have the Synapse default view column "type" present in your view. After running this function, changes may take a few minutes to propagate through Synapse.

Usage

update_study_annotations(study_table_id, fileview_id, annotations, dry_run = T)

Arguments

study_table_id	The synapse id of the portal study table.
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.
annotations	A vector of annotations to gather from the study table, and assign to the files.
dry_run	Default = TRUE Skips upload of annotations unless set to FALSE.

Value

If dry_run == T, returns updated annotations as a tibble.

Examples

## Not run: 
update_study_annotations(study_table_id = "syn16787123",
                         fileview_id = "syn16858331",
                         annotations = c("studyId","studyName","initiative","fundingAgency"),
                         dry_run = T)

## End(Not run)

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