Generate manifest via schematic service — manifest

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",
  access_token = Sys.getenv("SYNAPSE_AUTH_TOKEN")
)

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.
access_token: Synapse auth token, defaults to SYNAPSE_AUTH_TOKEN set in env.

Value

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