Takes a dataframe with string representations of FHIR bundles in the given column and outputs a dataframe of encoded resources.
pathling_encode_bundle(pc, df, resource_name, input_type = NULL, column = NULL)A Pathling context object.
A Spark DataFrame containing the bundles with the resources to encode.
The name of the FHIR resource to extract (Condition, Observation, etc.).
The MIME type of the input string encoding. Defaults to 'application/fhir+json'.
The column in which the resources to encode are stored. If 'NULL', then 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()
pc <- pathling_connect()
json_resources_df <- pathling_spark(pc) %>%
sparklyr::spark_read_text(path=system.file('extdata','bundle-xml', package='pathling'),
whole = TRUE)
pc %>% pathling_encode_bundle(json_resources_df, 'Condition',
input_type = MimeType$FHIR_XML, column = 'contents')
#> # Source: table<`sparklyr_tmp_0e92cbd4_cc5d_46bc_a67a_60d7f209a923`> [?? x 31]
#> # Database: spark_connection
#> id id_versioned meta implicitRules language text identifier
#> <chr> <chr> <lis> <chr> <chr> <lis> <list>
#> 1 2383c155-6345-e84… Condition/2… <lgl> NA NA <lgl> <lgl [1]>
#> 2 ccda8fb3-9f37-268… Condition/c… <lgl> NA NA <lgl> <lgl [1]>
#> 3 9d95d044-b2e6-0ee… Condition/9… <lgl> NA NA <lgl> <lgl [1]>
#> 4 5779b272-9e1b-317… Condition/5… <lgl> NA NA <lgl> <lgl [1]>
#> 5 a7988e15-0bb4-ffe… Condition/a… <lgl> NA NA <lgl> <lgl [1]>
#> 6 aebcc0e1-2ab0-2b9… Condition/a… <lgl> NA NA <lgl> <lgl [1]>
#> 7 857dc2db-94b9-73e… Condition/8… <lgl> NA NA <lgl> <lgl [1]>
#> 8 f2dac999-8ef5-8c3… Condition/f… <lgl> NA NA <lgl> <lgl [1]>
#> 9 4987db3c-2ef4-b32… Condition/4… <lgl> NA NA <lgl> <lgl [1]>
#> 10 217b8864-fed8-617… Condition/2… <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)