summarize_attribute: Helper summarization util

In nf-osi/nfportalutils: NF Portal Utilities

Helper summarization util

Description

Given some table X that provides values, summarize the values for an attribute and add summary as annotations on some entity. The entity could be X itself or another entity Y, e.g. a parent container entity. Example 1: With datasets, summarize species for all the files. Example 2: With projects, summarize dataType for all the files (in fact, see assign_study_data_types).

Usage

summarize_attribute(
  summary_query,
  attribute,
  entity_id = NULL,
  dry_run = TRUE,
  check_fun = NULL
)

Arguments

summary_query	Query (usually of a fileview) that returns appropriate aggregation per row. You may need to add group_concat, distinct, and or unnest to the query to get the correct list of distinct values depending on your data (e.g.⁠select group_concat(distinct unnest(tumorType)) as tumorType from ...⁠).
attribute	Name of attribute to update as annotation.
entity_id	Either a single valid Synapse id of the entity for which to update the attribute or a column present in summary_query that stores ids.
dry_run	Default = TRUE. Whether to update as well or just return list of annotation objects.
check_fun	An optional custom check function to apply to the values being updated in order for update to go through. Should return a boolean. Used only if dry_run = FALSE. It can be tailored towards the attribute/entity being updated (i.e. taking into account the schema and valid values).

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