meta_qc_dataset: QC dataset metadata with pass/fail result

In nf-osi/nfportalutils: NF Portal Utilities

QC dataset metadata with pass/fail result

Description

R wrapper for validation workflow with schematic. Because there is no validation-only service endpoint, we move metadata around twice (generating manifest from server and submitting back to server), so once schematic has a validation-only service endpoint that would be much more efficient. A dataset in this context is a folder, usually tagged with contentType = "dataset".

Usage

meta_qc_dataset(
  dataset_id,
  data_type = NULL,
  asset_view = "syn16787123",
  schema_url =
    "https://raw.githubusercontent.com/nf-osi/nf-metadata-dictionary/main/NF.jsonld",
  cleanup = TRUE
)

Arguments

dataset_id	Id of folder that represents a dataset, not actual Synapse dataset entity – see details.
data_type	A specific data type to validate against, otherwise tries to infer based on annotations. See details.
asset_view	A reference view, defaults to the main NF portal fileview.
schema_url	Schema URL, points by default to 'latest' main NF schema, can change to use a specific released version.
cleanup	Whether to automatically remove reconstituted manifests once done. Default TRUE.

Details

Note that we prefer to wrap the schematic web API over a local installation because:

• Will not require user to go through local schematic setup for this to be functional

• API more likely reflects an up-to-date version of schematic and consistent with current DCA deployment

When data_type can't be inferred based on annotations, this is treated as a fail.

Status: alpha and likely to change based on changes in schematic.

Value

List of structure list(result = result, notes = notes), where result indicates passing or NA if no data or if couldn't be validated for other reasons.

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