manifest_generate: Generate manifest via schematic service

In nf-osi/nfportalutils: NF Portal Utilities

Generate manifest via schematic service

Description

See schematic manifest generation. Note that this uses the access token of user that should already be logged in with syn_login.

Usage

manifest_generate(
  data_type,
  dataset_id = NULL,
  title = data_type,
  schema_url =
    "https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/main/NF.jsonld",
  asset_view = "syn16858331",
  output_format = "excel",
  use_annotations = TRUE,
  service = "https://schematic.api.sagebionetworks.org/v1/manifest/generate"
)

Arguments

data_type	Data type of the manifest to generate (aka Component).
dataset_id	Optional, if given this fills out manifest for existing dataset instead of generating a blank manifest.
title	Optional, custom title.
schema_url	Optional, defaults to main NF 'latest' data model.
asset_view	Optional, defaults to main NF portal fileview.
output_format	Format of 'excel', 'google_sheet', or 'dataframe'. Defaults to 'excel'.
use_annotations	Use annotations if filling out manifest for existing dataset. Defaults to TRUE for NF.
service	Service endpoint to use. Defaults to the schematic production endpoint.

Value

For excel, path to local file; for google_sheet, URL to sheet; for dataframe, JSON string of data.

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