add_to_collection: Add to collection

In nf-osi/nfportalutils: NF Portal Utilities

Add to collection

Description

Add items(s) to an existing collection, using the item(s)' current (latest) version. For datasets, the items should be files. For dataset collections, the items should be datasets. If an item attempting to be added happens to already be in the collection, this might lead to version conflicts, so the update will be rejected unless force is true.

Usage

add_to_collection(collection_id, items, check_items = FALSE, force = FALSE)

Arguments

collection_id	Collection id.
items	Character vector of one or more dataset entity ids to add.
check_items	Whether to check that ids are really appropriate item types and remove non-appropriate item types to help avoid Synapse errors (default FALSE because in most cases items are curated, and using check will be slower).
force	If some items are currently in the collection with a different version, should these items be force-added using current version? The safe default is FALSE to ensure any such updates are intentional.

Details

This is implemented with lower-level REST API because the Python client (as of v2.7) doesn't yet implement dataset collection class and methods (but dataset and relevant methods like add_item method are available). Thus, while this is generic enough to handle both datasets and dataset collections it is expected to be used more for dataset collections given that the dataset method is provided.

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