fhircrackr
Handling HL7 FHIR® Resources in R

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inst/doc/downloadResources.R

inst/doc/downloadResources.R
In fhircrackr: Handling HL7 FHIR® Resources in R 

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#"
)


hook_output = knitr::knit_hooks$get('output')
knitr::knit_hooks$set(output = function(x, options) {
	if (!is.null(n <- options$out.lines)){
	    if (any(nchar(x) > n)){
	    	index <- seq(1,nchar(x),n)
	    	x = substring(x, index, c(index[2:length(index)]-1, nchar(x)))
	    } 
	    x = paste(x, collapse = '\n# ')
	}
	hook_output(x, options)
})

# hook_warning = knitr::knit_hooks$get('warning')
# knitr::knit_hooks$set(warning = function(x, options) {
#     n <- 90
#     x = knitr:::split_lines(x)
#     # any lines wider than n should be wrapped
#     if (any(nchar(x) > n)) x = strwrap(x, width = n)
#     x = paste(x, collapse = '\n ')
#   hook_warning(x, options)
# })


## -----------------------------------------------------------------------------
library(fhircrackr)

## -----------------------------------------------------------------------------
fhir_url(url = "http://hapi.fhir.org/baseR4", resource = "Patient")

## ----warning=FALSE------------------------------------------------------------
fhir_resource_type(string = "Patient") #correct

fhir_resource_type(string = "medicationstatement") #fixed

fhir_resource_type(string = "medicationstatement", fix_capitalization = FALSE) #not fixed

fhir_resource_type(string = "Hospital") #an unknown resource type, a warning is issued
# Warning:
# In fhir_resource_type("Hospital") :
#   You gave "Hospital" as the resource type.
# This doesn't match any of the resource types defined under
# https://hl7.org/FHIR/resourcelist.html.
# If you are sure the resource type is correct anyway, you can ignore this warning.

## ---- out.lines=110-----------------------------------------------------------
request <- fhir_url(
	url        = "http://hapi.fhir.org/baseR4",
	resource   = "Patient",
	parameters = list(
		"birthdate" = "lt2000-01-01",
		"code"      = "http://loinc.org|1751-1"))

request

## ---- eval=F------------------------------------------------------------------
#  request <- fhir_url(url = "https://hapi.fhir.org/baseR4", resource = "Patient")
#  
#  patient_bundles <- fhir_search(request = request, max_bundles = 2, verbose = 0)

## ---- include=F---------------------------------------------------------------
patient_bundles <- fhir_unserialize(bundles = patient_bundles)

## ----results='hide'-----------------------------------------------------------
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"/ ...
# ...

## -----------------------------------------------------------------------------
request <- fhir_url(
	url        = "https://hapi.fhir.org/baseR4/",
	resource   = "MedicationStatement",
	parameters = list(
		"code"     = "http://snomed.info/ct|429374003",
		"_include" = "MedicationStatement:subject"))

## ---- eval=F------------------------------------------------------------------
#  medication_bundles <- fhir_search(request = request, max_bundles = 3)

## ---- include=F---------------------------------------------------------------
medication_bundles <- fhir_unserialize(bundles = medication_bundles)

## ---- eval=F------------------------------------------------------------------
#  fhir_save(bundles = medication_bundles, directory = "MyProject/medicationBundles")

## -----------------------------------------------------------------------------
ids <- c("72622884-0a09-4ea9-9a91-685bce3b0fe3", 
		 "2ca48b68-a641-4be7-a39d-9ffe2691a29a", 
		 "8bcdd92d-5f96-4e07-9f6a-e22a3591ee30",
		 "2067558f-c9ed-489a-9c2f-7387bb3426a2", 
		 "5077b4b0-07c9-4d03-b9ec-1f9f218f8239")

## -----------------------------------------------------------------------------
id_strings <- paste(ids, collapse = ",")

## -----------------------------------------------------------------------------
#note the list()-expression
body <- fhir_body(content = list(
	"identifier"  = id_strings,
	"_revinclude" = "Observation:patient"))

## ---- eval = F----------------------------------------------------------------
#  url <- fhir_url(url = "https://hapi.fhir.org/baseR4/", resource = "Patient")
#  
#  bundles <- fhir_search(request = url, body = body)

## ---- eval=F------------------------------------------------------------------
#  medication_bundles <- fhir_search(
#  	request     = request,
#  	max_bundles = 3,
#  	log_errors  = "myErrorFile")

## -----------------------------------------------------------------------------
#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
save(serialized_bundles, file = paste0(temp_dir, "/bundles.rda"))


## -----------------------------------------------------------------------------
#load bundles
load(paste0(temp_dir, "/bundles.rda"))

## ----results='hide'-----------------------------------------------------------
#unserialize
bundles <- fhir_unserialize(bundles = serialized_bundles)

#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)

## ---- eval=FALSE--------------------------------------------------------------
#  request <- fhir_url(url = "http://hapi.fhir.org/baseR4",
#  					resource = "Patient",
#  					parameters = c("_elements" = "name,gender,birthDate",
#  								   "_count"= "2"))
#  
#  
#  bundles <- fhir_search(request, max_bundles = 1)
#  
#  cat(toString(bundles[[1]]))

## -----------------------------------------------------------------------------
# <Bundle>
#   <id value="8e0db3ce-817b-48cd-ba3e-1a0d20f64366"/>
#   <meta>
#     <lastUpdated value="2022-03-31T08:48:55.934+00:00"/>
#   </meta>
#   <type value="searchset"/>
#   <link>
#     <relation value="self"/>
#     <url value="http://hapi.fhir.org/baseR4/Patient?_count=2&amp;_elements=name%2Cgender%2CbirthDate"/>
#   </link>
#   <link>
#     <relation value="next"/>
#     <url value="http://hapi.fhir.org/baseR4?_getpages=8e0db3ce-817b-48cd-ba3e-1a0d20f64366&amp;_getpagesoffset=2&amp;_count=2&amp;_pretty=true&amp;_bundletype=searchset&amp;_elements=birthDate,gender,name"/>
#   </link>
#   <entry>
#     <fullUrl value="http://hapi.fhir.org/baseR4/Patient/2564886"/>
#     <resource>
#       <Patient>
#         <id value="2564886"/>
#         <meta>
#           <versionId value="1"/>
#           <lastUpdated value="2021-09-28T01:04:35.774+00:00"/>
#           <source value="#rxRuwftRVG3erMwy"/>
#           <tag>
#             <system value="http://terminology.hl7.org/CodeSystem/v3-ObservationValue"/>
#             <code value="SUBSETTED"/>
#             <display value="Resource encoded in summary mode"/>
#           </tag>
#         </meta>
#         <name>
#           <text value="반영훈 사원"/>
#           <family value="반"/>
#           <given value="영훈"/>
#           <prefix value="사원"/>
#         </name>
#         <gender value="male"/>
#         <birthDate value="1992-01-12"/>
#       </Patient>
#     </resource>
#     <search>
#       <mode value="match"/>
#     </search>
#   </entry>
#   <entry>
#     <fullUrl value="http://hapi.fhir.org/baseR4/Patient/2564911"/>
#     <resource>
#       <Patient>
#         <id value="2564911"/>
#         <meta>
#           <versionId value="1"/>
#           <lastUpdated value="2021-09-28T01:12:59.207+00:00"/>
#           <source value="#rmWF4JDz6p1WVwzl"/>
#           <security>
#             <system value="http://terminology.hl7.org/CodeSystem/v2-0203"/>
#             <code value="RM"/>
#           </security>
#           <tag>
#             <system value="http://terminology.hl7.org/CodeSystem/v2-0203sbtest05"/>
#             <code value="SBTest05m"/>
#           </tag>
#           <tag>
#             <system value="http://terminology.hl7.org/CodeSystem/v3-ObservationValue"/>
#             <code value="SUBSETTED"/>
#             <display value="Resource encoded in summary mode"/>
#           </tag>
#         </meta>
#         <name>
#           <use value="usual"/>
#           <text value="human name"/>
#           <family value="Jonathan"/>
#           <given value="token_sort_test_data05"/>
#         </name>
#         <gender value="male"/>
#         <birthDate value="2021-09-01"/>
#       </Patient>
#     </resource>
#     <search>
#       <mode value="match"/>
#     </search>
#   </entry>
# </Bundle>

## ---- eval=F------------------------------------------------------------------
#  request <- fhir_url(url = "http://hapi.fhir.org/baseR4", resource = "Patient")
#  
#  fhir_search(
#  	request      = request,
#  	max_bundles  = 10,
#  	save_to_disc = "MyProject/downloadedBundles"
#  	)
#  
#  bundles<- fhir_load(directory = "MyProject/downloadedBundles")

## ---- include=F---------------------------------------------------------------
assign(x = "last_next_link", value = fhir_url( "http://hapi.fhir.org/baseR4?_getpages=0be4d713-a4db-4c27-b384-b772deabcbc4&_getpagesoffset=200&_count=20&_pretty=true&_bundletype=searchset"), envir = fhircrackr:::fhircrackr_env)


## -----------------------------------------------------------------------------
strsplit(fhir_next_bundle_url(), "&")

## ---- eval=F------------------------------------------------------------------
#  #Starting fhir search request
#  url <- fhir_url(
#  	url        = "http://hapi.fhir.org/baseR4",
#  	resource   = "Observation",
#  	parameters = list("_count" = "500"))
#  
#  count <- 0
#  
#  table_description <- fhir_table_description(resource = "Observation")
#  
#  while(!is.null(url)){
#  	
#  	#load 10 bundles
#  	bundles <- fhir_search(request = url, max_bundles = 10)
#  	
#  	#crack bundles
#  	dfs <- fhir_crack(bundles = bundles, design = table_description)
#  	
#  	#save cracked bundle to RData-file (can be exchanged by other data type)
#  	save(tables, file = paste0(tempdir(), "/table_", count, ".RData"))
#  	
#  	#retrieve starting point for next 10 bundles
#  	url <- fhir_next_bundle_url()
#  	
#  	count <- count + 1
#  	# if(count >= 20) {break}
#  }
#  

## ---- eval = FALSE------------------------------------------------------------
#  # define list of Patient resource ids
#  ids <- c("4b7736c3-c005-4383-bf7c-99710811efd9", "bef39d3a-62bb-48c0-83ff-3bb70b51d831",
#  		 "f371ed2f-5cb0-4093-a491-9df6e6bfcdf2", "277c4631-955e-4b52-bd40-78ddcde333b1",
#  		 "72173a13-d32f-4489-a7b4-dfc301df087f", "4a97acec-028e-4b45-a72f-2b7e08cf80ba")
#  
#  #split into smaller chunks of 2
#  id_list <- split(ids, ceiling(seq_along(ids)/2))
#  
#  #Define function that downloads one chunk of patients and serializes the result
#  extract_and_serialize <- function(x){
#                              b <- fhir_get_resources_by_ids(base_url = "http://hapi.fhir.org/baseR4",
#                                                             resource = "Patient",
#                                                             ids = x)
#                              fhir_serialize(b)
#  }
#  
#  #Download using 2 cores on linux:
#  bundles_serialized <- parallel::mclapply(
#  	X = pat_list,
#  	FUN = extract_and_serialize,
#      mc.cores = 2
#  )
#  
#  #Unserialize the resulting list and create one fhir_bundle_list object from it
#  bundles_unserialized <- lapply(bundles_serialized, fhir_unserialize)
#  result <- fhir_bundle_list(unlist(bundles_unserialized, recursive = FALSE))
#  

## ---- eval=FALSE--------------------------------------------------------------
#  #Download all Encounters
#  encounter_bundles <- fhir_search(request = "http://hapi.fhir.org/baseR4/Encounter")
#  
#  #Flatten
#  encounter_table <- fhir_crack(
#  	bundles = encounter_bundles,
#  	design = fhir_table_description(resource = "Encounter")
#  )
#  
#  #Extract Patient ids
#  pat_ids <- sub("Patient/", "", encounter_table$subject.reference)
#  
#  #Split into chunks of 20
#  pat_id_list <- split(pat_ids, ceiling(seq_along(pat_ids)/20))
#  
#  #Define function that downloads one chunk and serializes the result
#  extract_and_serialize <- function(x){
#                              b <- fhir_get_resources_by_ids(base_url = "http://hapi.fhir.org/baseR4",
#                              							   resource = "Patient",
#                                                             ids = x)
#                              fhir_serialize(b)
#  }
#  
#  #Download using 4 cores on linux:
#  bundles_serialized <- parallel::mclapply(
#  	X = pat_id_list,
#  	FUN = extract_and_serialize,
#      mc.cores = 4
#  )
#  
#  #Unserialize the resulting list and create one fhir_bundle_list object from it
#  bundles_unserialized <- lapply(bundles_serialized, fhir_unserialize)
#  result <- fhir_bundle_list(unlist(bundles_unserialized, recursive = FALSE))
#  

## ---- eval=F------------------------------------------------------------------
#  bundle <- fhir_sample_resources(
#  	base_url    = "http://hapi.fhir.org/baseR4",
#  	resource    = "Patient",
#  	parameters  = c(gender = "female", birthdate = "lt1960-01-01"),
#  	sample_size = 10
#  )

## ---- include=F---------------------------------------------------------------
bundle <- fhir_unserialize(fhircrackr:::female_pat_bundle)

## -----------------------------------------------------------------------------
pat <- fhir_table_description(resource = "Patient",
							  cols = c("id", "gender", "birthDate"))

fhir_crack(bundles = bundle, design = pat)

## ---- eval=F------------------------------------------------------------------
#  cap <- fhir_capability_statement(url = "http://hapi.fhir.org/baseR4")

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fhircrackr documentation built on Feb. 16, 2023, 8:33 p.m.

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