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,
depth = 1L
)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.- depth
How much deeper to go when there appears to be no files in the immediate scope. Defaults to 1L.
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.
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.