Create a data source from FHIR bundles — pathling_read_bundles • pathling

Creates a data source from a directory containing FHIR bundles.

pathling_read_bundles(pc, path, resource_types, mime_type = MimeType$FHIR_JSON)

Arguments

pc: The PathlingContext object.
path: The URI of the directory containing the bundles.
resource_types: A sequence of resource type codes that should be extracted from the bundles.
mime_type: The MIME type of the bundles. Defaults to "application/fhir+json".

Value

A DataSource object that can be used to run queries against the data.

See also

Pathling documentation - Reading Bundles

Other data source functions: pathling_read_datasets(), pathling_read_delta(), pathling_read_ndjson(), pathling_read_parquet(), pathling_read_tables()

Examples

pc <- pathling_connect()
data_source <- pc %>% pathling_read_bundles(pathling_examples('bundle-xml'),
     c("Patient", "Observation"), MimeType$FHIR_XML)
data_source %>% ds_read('Observation') %>% sparklyr::sdf_nrow()
#> [1] 61
pathling_disconnect(pc)