Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----eval=F-------------------------------------------------------------------
# install.packages("fhircrackr")
# library(fhircrackr)
## ----include=F----------------------------------------------------------------
library(fhircrackr)
## ----eval=F-------------------------------------------------------------------
# request <- fhir_url(url = "http://fhir.hl7.de:8080/baseDstu3", resource = "Patient")
# patient_bundles <- fhir_search(request = request, max_bundles = 2, verbose = 0)
## ----include=F----------------------------------------------------------------
patient_bundles <- fhir_unserialize(bundles = fhircrackr::patient_bundles)
## ----results='hide'-----------------------------------------------------------
length(patient_bundles)
#> [1] 2
patient_bundles
#> An object of class "fhir_bundle_list"
#> [[1]]
#> A fhir_bundle_xml object
#> No. of entries : 20
#> Self Link: http://hapi.fhir.org/baseR4/Patient
#> Next Link: http://hapi.fhir.org/baseR4?_getpages=ce958386-53d0-4042-888c-cad53bf5d5a1 ...
#>
#> {xml_node}
#> <Bundle>
#> [1] <id value="ce958386-53d0-4042-888c-cad53bf5d5a1"/>
#> [2] <meta>\n <lastUpdated value="2021-05-10T12:12:43.317+00:00"/>\n</meta>
#> [3] <type value="searchset"/>
#> [4] <link>\n <relation value="self"/>\n <url value="http://hapi.fhir.org/b ...
#> [5] <link>\n <relation value="next"/>\n <url value="http://hapi.fhir.org/b ...
#> [6] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837602"/ ...
#> [7] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/example-r ...
#> [8] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837624"/ ...
#> [9] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837626"/ ...
#> [10] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837631"/ ...
#> [11] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837716"/ ...
#> [12] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837720"/ ...
#> [13] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837714"/ ...
#> [14] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837721"/ ...
#> [15] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837722"/ ...
#> [16] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837723"/ ...
#> [17] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837724"/ ...
#> [18] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/cfsb16116 ...
#> [19] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837736"/ ...
#> [20] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837737"/ ...
#> ...
#>
#> [[2]]
#> A fhir_bundle_xml object
#> No. of entries : 20
#> Self Link: http://hapi.fhir.org/baseR4?_getpages=ce958386-53d0-4042-888c-cad53bf5d5a1 ...
#> Next Link: http://hapi.fhir.org/baseR4?_getpages=ce958386-53d0-4042-888c-cad53bf5d5a1 ...
#>
#> {xml_node}
#> <Bundle>
#> [1] <id value="ce958386-53d0-4042-888c-cad53bf5d5a1"/>
#> [2] <meta>\n <lastUpdated value="2021-05-10T12:12:43.317+00:00"/>\n</meta>
#> [3] <type value="searchset"/>
#> [4] <link>\n <relation value="self"/>\n <url value="http://hapi.fhir.org/b ...
#> [5] <link>\n <relation value="next"/>\n <url value="http://hapi.fhir.org/b ...
#> [6] <link>\n <relation value="previous"/>\n <url value="http://hapi.fhir.o ...
#> [7] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837760"/ ...
#> [8] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837766"/ ...
#> [9] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837768"/ ...
#> [10] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837781"/ ...
#> [11] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837783"/ ...
#> [12] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837784"/ ...
#> [13] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837787"/ ...
#> [14] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837788"/ ...
#> [15] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837789"/ ...
#> [16] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837790"/ ...
#> [17] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837791"/ ...
#> [18] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837792"/ ...
#> [19] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837793"/ ...
#> [20] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837794"/ ...
#> ...
## -----------------------------------------------------------------------------
#define table_description
table_description <- fhir_table_description(
resource = "Patient",
cols = c(
id = "id",
use_name = "name/use",
given_name = "name/given",
family_name = "name/family",
gender = "gender",
birthday = "birthDate"
),
sep = " ~ ",
brackets = c("<<", ">>"),
rm_empty_cols = FALSE,
format = 'compact',
keep_attr = FALSE
)
#have a look
table_description
## -----------------------------------------------------------------------------
#flatten resources
patients <- fhir_crack(bundles = patient_bundles, design = table_description, verbose = 0)
#have look at the results
head(patients)
## -----------------------------------------------------------------------------
bundles <- fhir_unserialize(bundles = example_bundles1)
## -----------------------------------------------------------------------------
table_description <- fhir_table_description(
resource = "Patient",
brackets = c("[", "]"),
sep = " | ",
rm_empty_cols = FALSE,
format = 'compact',
keep_attr = FALSE
)
df <- fhir_crack(bundles = bundles, design = table_description, verbose = 0)
df
## -----------------------------------------------------------------------------
table_description <- fhir_table_description(
resource = "Patient",
cols = c(
id = "id",
city = "address[use[@value='home']]/city",
type = "address[use[@value='home']]/type",
country = "address[use[@value='home']]/country",
name = "name/given"
)
)
df_filtered <- fhir_crack(bundles = bundles, design = table_description, verbose = 0)
df_filtered
## -----------------------------------------------------------------------------
fhir_melt(
indexed_data_frame = df,
columns = "address.city",
brackets = c("[", "]"),
sep = " | ",
all_columns = FALSE
)
## -----------------------------------------------------------------------------
cols <- c("address.city", "address.use", "address.type", "address.country")
fhir_melt(
indexed_data_frame = df,
columns = cols,
brackets = c("[", "]"),
sep = " | ",
all_columns = FALSE
)
## -----------------------------------------------------------------------------
molten <- fhir_melt(
indexed_data_frame = df,
columns = cols,
brackets = c("[", "]"),
sep = " | ",
all_columns = TRUE
)
molten
## -----------------------------------------------------------------------------
fhir_rm_indices(indexed_data_frame = molten, brackets = c("[", "]"))
## -----------------------------------------------------------------------------
#serialize bundles
serialized_bundles <- fhir_serialize(bundles = patient_bundles)
#have a look at them
head(serialized_bundles[[1]])
## -----------------------------------------------------------------------------
#create temporary directory for saving
temp_dir <- tempdir()
#save
saveRDS(serialized_bundles, file = paste0(temp_dir, "/bundles.rda"))
## -----------------------------------------------------------------------------
#load bundles
serialized_bundles_reloaded <- readRDS(paste0(temp_dir, "/bundles.rda"))
## ----results='hide'-----------------------------------------------------------
#unserialize
bundles <- fhir_unserialize(bundles = serialized_bundles_reloaded)
#have a look
bundles
#> An object of class "fhir_bundle_list"
#> [[1]]
#> A fhir_bundle_xml object
#> No. of entries : 20
#> Self Link: http://hapi.fhir.org/baseR4/Patient
#> Next Link: http://hapi.fhir.org/baseR4?_getpages=ce958386-53d0-4042-888c-cad53bf5d5a1 ...
#>
#> {xml_node}
#> <Bundle>
#> [1] <id value="ce958386-53d0-4042-888c-cad53bf5d5a1"/>
#> [2] <meta>\n <lastUpdated value="2021-05-10T12:12:43.317+00:00"/>\n</meta>
#> [3] <type value="searchset"/>
#> [4] <link>\n <relation value="self"/>\n <url value="http://hapi.fhir.org/b ...
#> [5] <link>\n <relation value="next"/>\n <url value="http://hapi.fhir.org/b ...
#> [6] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837602"/ ...
#> [7] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/example-r ...
#> [8] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837624"/ ...
#> [9] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837626"/ ...
#> [10] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837631"/ ...
#> [11] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837716"/ ...
#> [12] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837720"/ ...
#> [13] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837714"/ ...
#> [14] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837721"/ ...
#> [15] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837722"/ ...
#> [16] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837723"/ ...
#> [17] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837724"/ ...
#> [18] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/cfsb16116 ...
#> [19] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837736"/ ...
#> [20] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837737"/ ...
#> ...
#>
#> [[2]]
#> A fhir_bundle_xml object
#> No. of entries : 20
#> Self Link: http://hapi.fhir.org/baseR4?_getpages=ce958386-53d0-4042-888c-cad53bf5d5a1 ...
#> Next Link: http://hapi.fhir.org/baseR4?_getpages=ce958386-53d0-4042-888c-cad53bf5d5a1 ...
#>
#> {xml_node}
#> <Bundle>
#> [1] <id value="ce958386-53d0-4042-888c-cad53bf5d5a1"/>
#> [2] <meta>\n <lastUpdated value="2021-05-10T12:12:43.317+00:00"/>\n</meta>
#> [3] <type value="searchset"/>
#> [4] <link>\n <relation value="self"/>\n <url value="http://hapi.fhir.org/b ...
#> [5] <link>\n <relation value="next"/>\n <url value="http://hapi.fhir.org/b ...
#> [6] <link>\n <relation value="previous"/>\n <url value="http://hapi.fhir.o ...
#> [7] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837760"/ ...
#> [8] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837766"/ ...
#> [9] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837768"/ ...
#> [10] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837781"/ ...
#> [11] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837783"/ ...
#> [12] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837784"/ ...
#> [13] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837787"/ ...
#> [14] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837788"/ ...
#> [15] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837789"/ ...
#> [16] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837790"/ ...
#> [17] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837791"/ ...
#> [18] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837792"/ ...
#> [19] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837793"/ ...
#> [20] <entry>\n <fullUrl value="http://hapi.fhir.org/baseR4/Patient/1837794"/ ...
#> ...
## -----------------------------------------------------------------------------
#save bundles as xml files
fhir_save(bundles = patient_bundles, directory = temp_dir)
## -----------------------------------------------------------------------------
bundles <- fhir_load(directory = temp_dir)
## ----include=F----------------------------------------------------------------
file.remove(
paste0(
temp_dir,
c(
"/bundles.rda",
"/design.xml",
"/1.xml",
"/2.xml"
)
)
)
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