View source: R/annotation_qc.R
meta_qc_dataset | R Documentation |
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".
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
)
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 |
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
.
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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.