Replace httr with httr2 (#77)

* replace {httr} by {httr2} * Update CITATION.cff * fix linter and run devtools::document() * update test file for check_dhis2_attributes-helpers.R * use {httr2} to submit the query parameters * fix linters * allow for the query parameters to be specified as a list by the user * update the test files to account for the fact that the query parameters are provided as a list by the user * fix linters * use a different areaTypeId in the examples and tests * update the mock files * update test for readepi() * update test-readepi.R * fix issue with reading from DHIS2 * Automatic readme update * comment out the mock testing in Fingertips test files * use "%>%" instead of "|>" for harmonisation. * update the URL to the play DHIS2 instance --------- Co-authored-by: GitHub Action <[email protected]>
epiverse-trace · May 22, 2024 · cbef45d · cbef45d
1 parent 98f7e47
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diff --git a/CITATION.cff b/CITATION.cff
@@ -2,7 +2,7 @@
 # CITATION file created with {cffr} R package, v0.5.0
 # See also: https://docs.ropensci.org/cffr/
 # -----------------------------------------------------------
- 
+
 cff-version: 1.2.0
 message: 'To cite package "readepi" in publications use:'
 type: software
@@ -136,16 +136,16 @@ references:
     orcid: https://orcid.org/0000-0002-6983-2759
   year: '2024'
 - type: software
-  title: httr
-  abstract: 'httr: Tools for Working with URLs and HTTP'
+  title: httr2
+  abstract: 'httr2: Perform HTTP Requests and Process the Responses'
   notes: Imports
-  url: https://httr.r-lib.org/
-  repository: https://CRAN.R-project.org/package=httr
+  url: https://httr2.r-lib.org
+  repository: https://CRAN.R-project.org/package=httr2
   authors:
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@posit.co
-  year: '2024'
+    email: hadley@rstudio.com
+  year: '2023'
 - type: software
   title: magrittr
   abstract: 'magrittr: A Forward-Pipe Operator for R'
@@ -164,7 +164,7 @@ references:
   title: odbc
   abstract: 'odbc: Connect to ODBC Compatible Databases (using the DBI Interface)'
   notes: Imports
-  url: https://odbc.r-dbi.org
+  url: https://r-dbi.github.io/odbc/
   repository: https://CRAN.R-project.org/package=odbc
   authors:
   - family-names: Hester

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,7 +29,7 @@ Imports:
     dplyr,
     fingertipsR (>= 1.0.10.9001),
     glue,
-    httr,
+    httr2,
     magrittr,
     odbc,
     pool,

diff --git a/R/check_dhis2_attributes-helpers.R b/R/check_dhis2_attributes-helpers.R
@@ -18,7 +18,7 @@
 #' @examples
 #' \dontrun{
 #'   response <- dhis2_make_api_request(
-#'     base_url  = file.path("https:/", "play.dhis2.org", "dev"),
+#'     base_url  = file.path("https:/", "play.dhis2.org", "demo"),
 #'     user_name = "admin",
 #'     password  = "district",
 #'     which     = "dataElements"
@@ -28,25 +28,26 @@
 dhis2_make_api_request <- function(base_url,
                                    user_name,
                                    password,
-                                   which     = "dataElements") {
+                                   which = "dataElements") {
   url <- file.path(
     base_url,
     "api",
-    which,
-    "?fields=id,name,shortName&paging=false"
+    glue::glue(which, "?fields=id,name,shortName&paging=false")
   )
-  response <- httr::GET(url, httr::authenticate(user_name, password))
-  response
+  req <- httr2::request(url) %>%
+    httr2::req_auth_basic(user_name, password) %>%
+    httr2::req_perform()
+  req
 }
 
 #' Get the relevant dataset
 #'
 #' @param base_url the web address of the server the user wishes to log in to
 #' @param user_name the user name
 #' @param password the user's password
-#' @param attribute_id a comma-separated list of DHIS2 attribute ids. The ids
-#'    could be those of a dataSet or an organisationUnit.
-#' @param which the target DHIS2 attribute name
+#' @param attribute_id a vector of DHIS2 attribute ids. The ids
+#'    could be those of a dataSet or an orgUnit.
+#' @param which the target DHIS2 end point
 #'
 #' @return a `list` of 2 elements: a `character` string with the target
 #'    attributes ID(s) and a `data.frame` that contains the data of interest
@@ -55,10 +56,10 @@ dhis2_make_api_request <- function(base_url,
 #' @examples
 #' \dontrun{
 #' result <- dhis2_get_relevant_attributes(
-#'   base_url     = "https://play.dhis2.org/dev/",
+#'   base_url     = "https://play.dhis2.org/demo",
 #'   user_name    = "admin",
 #'   password     = "district",
-#'   attribute_id = "pBOMPrpg1QX,BfMAe6Itzgt",
+#'   attribute_id = c("pBOMPrpg1QX", "BfMAe6Itzgt"),
 #'   which        = "dataSets"
 #' )
 #' }
@@ -71,23 +72,22 @@ dhis2_get_relevant_attributes <- function(base_url,
   checkmate::assert_character(which,
                               len = 1L, any.missing = FALSE,
                               null.ok = FALSE)
-  checkmate::assert_character(attribute_id,
-                              len = 1L, any.missing = FALSE,
-                              null.ok = TRUE)
-  checkmate::check_choice(which, c("dataSets", "organisationUnits",
-                                   "dataElementGroups", "dataElements"))
-  if (is.character(attribute_id)) {
-    attribute_id <- unlist(strsplit(attribute_id, ",", fixed = TRUE))
-  }
+  checkmate::assert_vector(attribute_id,
+                           min.len = 1L, any.missing = FALSE,
+                           null.ok = TRUE)
+  checkmate::check_choice(which, c("dataSets", "dataElementGroups",
+                                   "organisationUnits",
+                                   "organisationUnitGroups", "dataElements"))
+
   response   <- dhis2_make_api_request(base_url, user_name, password, which)
-  content    <- httr::content(response, as = "parsed")
+  content    <- httr2::resp_body_json(response)
   attributes <- content %>% dplyr::bind_rows()
   if (which != "dataElements") {
     idx <- which(attribute_id %in% attributes[["id"]])
     if (length(idx) == 0L) {
-      stop("Provided attribute ids not found!\n
-      Use readepi:::dhis2_make_api_request() function to view the list of
-      available attributes")
+      stop("Provided attribute ids not found!",
+           "Use readepi:::dhis2_make_api_request() function to view the list",
+           "of available attributes")
     }
     if (length(idx) < length(attribute_id)) {
       warning(
@@ -100,13 +100,15 @@ dhis2_get_relevant_attributes <- function(base_url,
 
   res <- switch(
     which,
-    dataSets          = list(dataset   = attribute_id,
-                             data_sets = attributes),
-    organisationUnits = list(organisation_unit = attribute_id,
-                             org_units         = attributes),
-    dataElementGroups = list(data_element_group = attribute_id,
-                             data_elt_groups    = attributes),
-    dataElements      = attributes
+    dataSets               = list(dataset   = attribute_id,
+                                  data_sets = attributes),
+    dataElementGroups      = list(data_element_group = attribute_id,
+                                  data_elt_groups    = attributes),
+    organisationUnits      = list(organisation_unit = attribute_id,
+                                  org_units         = attributes),
+    organisationUnitGroups = list(organisation_unit_group = attribute_id,
+                                  org_units_groups        = attributes),
+    dataElements           = attributes
   )
   res
 }
@@ -125,7 +127,7 @@ dhis2_get_relevant_attributes <- function(base_url,
 #' @examples
 #' \dontrun{
 #' datasets <- dhis2_get_attributes(
-#'   base_url  = "https://play.dhis2.org/dev/",
+#'   base_url  = "https://play.dhis2.org/demo/",
 #'   user_name = "admin",
 #'   password  = "district",
 #'   which     = "dataSets"
@@ -148,7 +150,7 @@ dhis2_get_attributes <- function(base_url,
   checkmate::check_choice(which, c("dataSets", "organisationUnits",
                                    "dataElementGroups", "dataElements"))
   response   <- dhis2_make_api_request(base_url, user_name, password, which)
-  content    <- httr::content(response, as = "parsed")
+  content    <- httr2::resp_body_json(response)
   attributes <- content %>% dplyr::bind_rows()
   attributes
 }
diff --git a/R/check_dhis2_attributes.R b/R/check_dhis2_attributes.R
@@ -3,39 +3,35 @@
 #' @param base_url the web address of the server the user wishes to log in to
 #' @param user_name the user name
 #' @param password the user's password
-#' @param dataset the dataSets identifiers
-#' @param organisation_unit the organisationUnits identifiers
-#' @param data_element_group the dataElementGroups identifiers
+#' @param query_parameters a list with the parameters that will be used to
+#'    determine which data is returned by the query
 #'
-#' @return a list of 7 elements of type `character`.
+#' @return a list of 9 elements of type `character`.
 #'
 #' @examples
 #' \dontrun{
-#' attributes <- dhis2_check_attributes(
-#'   base_url            = "https://play.dhis2.org/dev/",
-#'   user_name           = "admin",
-#'   password            = "district",
-#'   dataset             = "pBOMPrpg1QX",
-#'   organisation_unit   = "DiszpKrYNg8",
-#'   data_element_group  = NULL
-#' )
+#'   attributes <- dhis2_check_attributes(
+#'     base_url         = "https://play.dhis2.org/dev",
+#'     user_name        = "admin",
+#'     password         = "district",
+#'     query_parameters = list(dataSet = "pBOMPrpg1QX",
+#'                             orgUnit = "DiszpKrYNg8")
+#'   )
 #' }
 #'
 #' @keywords internal
 #'
 dhis2_check_attributes <- function(base_url,
                                    user_name,
                                    password,
-                                   dataset,
-                                   organisation_unit  = NULL,
-                                   data_element_group = NULL) {
+                                   query_parameters) {
   # get the relevant dataset
-  if (!is.null(dataset)) {
+  if ("dataSet" %in% names(query_parameters)) {
     tmp_res   <- dhis2_get_relevant_attributes(
       base_url     = base_url,
       user_name    = user_name,
       password     = password,
-      attribute_id = dataset,
+      attribute_id = query_parameters[["dataSet"]],
       which        = "dataSets"
     )
     dataset   <- tmp_res[["dataset"]]
@@ -44,13 +40,28 @@ dhis2_check_attributes <- function(base_url,
     dataset   <- data_sets <- NULL
   }
 
+  # get the relevant data element groups
+  if ("dataElementGroup" %in% names(query_parameters)) {
+    tmp_res <- dhis2_get_relevant_attributes(
+      base_url     = base_url,
+      user_name    = user_name,
+      password     = password,
+      attribute_id = query_parameters[["dataElementGroup"]],
+      which        = "dataElementGroups"
+    )
+    data_element_group <- tmp_res[["data_element_group"]]
+    data_elt_groups    <- tmp_res[["data_elt_groups"]]
+  } else {
+    data_element_group <- data_elt_groups <- NULL
+  }
+
   # get the relevant organisation units
-  if (!is.null(organisation_unit)) {
+  if ("orgUnit" %in% names(query_parameters)) {
     tmp_res   <- dhis2_get_relevant_attributes(
       base_url     = base_url,
       user_name    = user_name,
       password     = password,
-      attribute_id = organisation_unit,
+      attribute_id = query_parameters[["orgUnit"]],
       which        = "organisationUnits"
     )
     organisation_unit <- tmp_res[["organisation_unit"]]
@@ -59,19 +70,19 @@ dhis2_check_attributes <- function(base_url,
     organisation_unit <- org_units <- NULL
   }
 
-  # get the relevant data element groups
-  if (!is.null(data_element_group)) {
-    tmp_res <- dhis2_get_relevant_attributes(
+  # get the relevant organisation units
+  if ("orgUnitGroup" %in% names(query_parameters)) {
+    tmp_res   <- dhis2_get_relevant_attributes(
       base_url     = base_url,
       user_name    = user_name,
       password     = password,
-      attribute_id = data_element_group,
-      which        = "dataElementGroups"
+      attribute_id = query_parameters[["orgUnitGroup"]],
+      which        = "organisationUnitGroups"
     )
-    data_element_group <- tmp_res[["data_element_group"]]
-    data_elt_groups    <- tmp_res[["data_elt_groups"]]
+    organisation_unit_group <- tmp_res[["organisation_unit_group"]]
+    org_units_groups        <- tmp_res[["org_units_groups"]]
   } else {
-    data_element_group <- data_elt_groups <- NULL
+    organisation_unit_group <- org_units_groups <- NULL
   }
 
   # get the data element
@@ -90,6 +101,8 @@ dhis2_check_attributes <- function(base_url,
     org_units_details           = org_units,
     data_element_group          = data_element_group,
     data_element_groups_details = data_elt_groups,
+    organisation_unit_group     = organisation_unit_group,
+    org_units_groups            = org_units_groups,
     data_elements               = data_elements
   )
 }