Takes a Spark DataFrame with string representations of FHIR resources in the given column and encodes the resources of the given types as Spark DataFrame.
pathling_encode(pc, df, resource_name, input_type = NULL, column = NULL)The Pathling context object.
A Spark DataFrame containing the resources to encode.
The name of the FHIR resource to extract (e.g., "Condition", "Observation").
The MIME type of input string encoding. Defaults to "application/fhir+json".
The column in which the resources to encode are stored. If set to NULL, the input DataFrame is assumed to have one column of type string.
A Spark DataFrame containing the given type of resources encoded into Spark columns.
Other encoding functions:
pathling_encode_bundle()
pc <- pathling_connect()
json_resources_df <- pathling_spark(pc) %>%
sparklyr::spark_read_text(path=system.file('extdata','ndjson', 'Condition.ndjson',
package='pathling'))
pc %>% pathling_encode(json_resources_df, 'Condition')
#> # Source: table<`sparklyr_tmp_c2bee0c3_15ae_4517_aee5_423b5f934e7f`> [?? x 31]
#> # Database: spark_connection
#> id id_versioned meta implicitRules language text identifier
#> <chr> <chr> <lis> <chr> <chr> <lis> <list>
#> 1 c879c300-7fdf-4b5… Condition/c… <lgl> NA NA <lgl> <lgl [1]>
#> 2 bb9c4fc1-795a-449… Condition/b… <lgl> NA NA <lgl> <lgl [1]>
#> 3 e620d7ee-6cfe-4f0… Condition/e… <lgl> NA NA <lgl> <lgl [1]>
#> 4 0447de38-1f2a-411… Condition/0… <lgl> NA NA <lgl> <lgl [1]>
#> 5 4025ceb3-04a6-41f… Condition/4… <lgl> NA NA <lgl> <lgl [1]>
#> 6 7ed34fb1-0bbf-4c4… Condition/7… <lgl> NA NA <lgl> <lgl [1]>
#> 7 5ef84858-0480-4a3… Condition/5… <lgl> NA NA <lgl> <lgl [1]>
#> 8 5378726d-7f2b-4c8… Condition/5… <lgl> NA NA <lgl> <lgl [1]>
#> 9 31393667-dd7f-4c9… Condition/3… <lgl> NA NA <lgl> <lgl [1]>
#> 10 6464e20b-55ec-468… Condition/6… <lgl> NA NA <lgl> <lgl [1]>
#> # ℹ more rows
#> # ℹ 24 more variables: clinicalStatus <list>, verificationStatus <list>,
#> # category <list>, severity <list>, code <list>, bodySite <list>,
#> # subject <list>, encounter <list>, onsetAge <list>, onsetDateTime <chr>,
#> # onsetPeriod <list>, onsetRange <list>, onsetString <chr>,
#> # abatementAge <list>, abatementDateTime <chr>, abatementPeriod <list>,
#> # abatementRange <list>, abatementString <chr>, recordedDate <chr>, …
pathling_disconnect(pc)