R/MetadataClient.r
In naturalis/nbaR: R Package Client for the Netherlands Biodiversity API
# Netherlands Biodiversity API
#
# Access to the digitised Natural History collection at the Naturalis Biodiversity Center
#
# OpenAPI spec version: v2
# Contact: support@naturalis.nl
# Generated by: https://github.com/swagger-api/swagger-codegen.git
#' @title Metadata operations
#' @description This client connects to all Metadata-related endpoints
#' of the NBA. Each endpoint is available as a class method
#' (see section 'Methods' below). Optionally, a custom URL
#' pointing to a NBA server and a user Agent can be specified
#' by the user (see section 'Fields' below).
#'
#' @docType class
#'
#' @format R6 class
#'
#' @field basePath Stores url path of the request, defaults to http://api.biodiversitydata.nl/v2
#' @field userAgent Set the user agent of the request, defaults to nbaR/0.1.0
#'
#' @importFrom R6 R6Class
#'
#' @usage
#' # client <- MetadataClient$new()
#'
#' @section Methods:
#' \describe{
#' \item{\code{ get_allowed_date_formats }}{
#'
#' Get allowed values for dates in queries;
#' Queries with other formatted dates will result in a query error.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_list_phase_or_stage }}{
#'
#' Get allowed values for the field 'PhaseOrStage' in a specimen document;
#' See also endpoint /getControlledLists.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_list_sex }}{
#'
#' Get allowed values for the field 'Sex' in a specimen document;
#' See also endpoint /getControlledLists.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_list_specimen_type_status }}{
#'
#' Get allowed values for the field 'SpecimenTypeStatus' in a specimen document;
#' See also endpoint /getControlledLists.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_list_taxonomic_status }}{
#'
#' Get allowed values for the field 'TaxonomicStatus' in specimen and taxon documents;
#' See also endpoint /getControlledLists.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_lists }}{
#'
#' Get the names of fields for which a controlled vocabulary exists;
#' Possible values for fields with controlled vocabularies can be queried with metadata/getControlledList/{field}.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_rest_services }}{
#'
#' List all available REST services and their parameters;
#' Lists end point name, http method, response type, and URL.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ RestService }
#' }
#' \item{\code{ get_setting }}{
#'
#' Get the value of an NBA setting;
#' All settings can be queried with /metadata/getSettings.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ name } : name of setting
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_settings }}{
#'
#' List all publicly available configuration settings for the NBA;
#' The value of a specific setting can be queried with metadata/getSetting/{name}.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_source_systems }}{
#'
#' Get the data sources from which the data was retrieved;
#' Returns code and name of all source systems.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ SourceSystem }
#' }
#' }
#'
#' @export
MetadataClient <- R6::R6Class(
"MetadataClient",
inherit = ApiClient,
public = list(
initialize = function(basePath, userAgent) {
super$initialize(basePath, userAgent)
},
get_allowed_date_formats = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getAllowedDateFormats"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_list_phase_or_stage = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledList/PhaseOrStage"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_list_sex = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledList/Sex"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_list_specimen_type_status = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledList/SpecimenTypeStatus"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_list_taxonomic_status = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledList/TaxonomicStatus"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_lists = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledLists"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_rest_services = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getRestServices"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is object of model class
returnObject <- RestService$new()
## API call result is "list container"
result <- lapply(
httr::content(response),
function(x) {
cl <- returnObject$clone()
cl$fromList(x,
typeMapping = list(item = private$getBaseDataType())
)
}
)
Response$new(result, response)
}
},
get_setting = function(
name = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getSetting/{name}"
if (!missing(`name`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "name", "\\}"), `name`, urlPath)
}
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.list(httr::content(response))
Response$new(result, response)
}
},
get_settings = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getSettings"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
get_source_systems = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getSourceSystems"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is object of model class
returnObject <- SourceSystem$new()
## API call result is "list container"
result <- lapply(
httr::content(response),
function(x) {
cl <- returnObject$clone()
cl$fromList(x,
typeMapping = list(item = private$getBaseDataType())
)
}
)
Response$new(result, response)
}
},
print = function(...) {
## print class name
cat("<MetadataClient>\n")
cat("\tInherits from: <ApiClient>\n\n")
## print all members with values
cat("Fields:\n")
cat("\tbasePath:\t", self$basePath, "\n")
cat("\tuserAgent:\t", self$userAgent, "\n")
## print all methods
cat("Methods:\n")
cat("\tget_allowed_date_formats", "\n")
cat("\tget_controlled_list_phase_or_stage", "\n")
cat("\tget_controlled_list_sex", "\n")
cat("\tget_controlled_list_specimen_type_status", "\n")
cat("\tget_controlled_list_taxonomic_status", "\n")
cat("\tget_controlled_lists", "\n")
cat("\tget_rest_services", "\n")
cat("\tget_setting", "\n")
cat("\tget_settings", "\n")
cat("\tget_source_systems", "\n")
cat("\tping\n")
invisible(self)
}
)
)
naturalis/nbaR documentation built on Nov. 12, 2023, 4:47 p.m.
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# Netherlands Biodiversity API
#
# Access to the digitised Natural History collection at the Naturalis Biodiversity Center
#
# OpenAPI spec version: v2
# Contact: support@naturalis.nl
# Generated by: https://github.com/swagger-api/swagger-codegen.git
#' @title Metadata operations
#' @description This client connects to all Metadata-related endpoints
#' of the NBA. Each endpoint is available as a class method
#' (see section 'Methods' below). Optionally, a custom URL
#' pointing to a NBA server and a user Agent can be specified
#' by the user (see section 'Fields' below).
#'
#' @docType class
#'
#' @format R6 class
#'
#' @field basePath Stores url path of the request, defaults to http://api.biodiversitydata.nl/v2
#' @field userAgent Set the user agent of the request, defaults to nbaR/0.1.0
#'
#' @importFrom R6 R6Class
#'
#' @usage
#' # client <- MetadataClient$new()
#'
#' @section Methods:
#' \describe{
#' \item{\code{ get_allowed_date_formats }}{
#'
#' Get allowed values for dates in queries;
#' Queries with other formatted dates will result in a query error.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_list_phase_or_stage }}{
#'
#' Get allowed values for the field 'PhaseOrStage' in a specimen document;
#' See also endpoint /getControlledLists.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_list_sex }}{
#'
#' Get allowed values for the field 'Sex' in a specimen document;
#' See also endpoint /getControlledLists.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_list_specimen_type_status }}{
#'
#' Get allowed values for the field 'SpecimenTypeStatus' in a specimen document;
#' See also endpoint /getControlledLists.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_list_taxonomic_status }}{
#'
#' Get allowed values for the field 'TaxonomicStatus' in specimen and taxon documents;
#' See also endpoint /getControlledLists.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_controlled_lists }}{
#'
#' Get the names of fields for which a controlled vocabulary exists;
#' Possible values for fields with controlled vocabularies can be queried with metadata/getControlledList/{field}.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ get_rest_services }}{
#'
#' List all available REST services and their parameters;
#' Lists end point name, http method, response type, and URL.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ RestService }
#' }
#' \item{\code{ get_setting }}{
#'
#' Get the value of an NBA setting;
#' All settings can be queried with /metadata/getSettings.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ name } : name of setting
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_settings }}{
#'
#' List all publicly available configuration settings for the NBA;
#' The value of a specific setting can be queried with metadata/getSetting/{name}.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_source_systems }}{
#'
#' Get the data sources from which the data was retrieved;
#' Returns code and name of all source systems.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ SourceSystem }
#' }
#' }
#'
#' @export
MetadataClient <- R6::R6Class(
"MetadataClient",
inherit = ApiClient,
public = list(
initialize = function(basePath, userAgent) {
super$initialize(basePath, userAgent)
},
get_allowed_date_formats = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getAllowedDateFormats"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_list_phase_or_stage = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledList/PhaseOrStage"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_list_sex = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledList/Sex"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_list_specimen_type_status = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledList/SpecimenTypeStatus"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_list_taxonomic_status = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledList/TaxonomicStatus"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_controlled_lists = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getControlledLists"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.character(httr::content(response))
Response$new(result, response)
}
},
get_rest_services = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getRestServices"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is object of model class
returnObject <- RestService$new()
## API call result is "list container"
result <- lapply(
httr::content(response),
function(x) {
cl <- returnObject$clone()
cl$fromList(x,
typeMapping = list(item = private$getBaseDataType())
)
}
)
Response$new(result, response)
}
},
get_setting = function(
name = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getSetting/{name}"
if (!missing(`name`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "name", "\\}"), `name`, urlPath)
}
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is "primitive type", return vector or single value
result <- as.list(httr::content(response))
Response$new(result, response)
}
},
get_settings = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getSettings"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
get_source_systems = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/metadata/getSourceSystems"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
## API call result is object of model class
returnObject <- SourceSystem$new()
## API call result is "list container"
result <- lapply(
httr::content(response),
function(x) {
cl <- returnObject$clone()
cl$fromList(x,
typeMapping = list(item = private$getBaseDataType())
)
}
)
Response$new(result, response)
}
},
print = function(...) {
## print class name
cat("<MetadataClient>\n")
cat("\tInherits from: <ApiClient>\n\n")
## print all members with values
cat("Fields:\n")
cat("\tbasePath:\t", self$basePath, "\n")
cat("\tuserAgent:\t", self$userAgent, "\n")
## print all methods
cat("Methods:\n")
cat("\tget_allowed_date_formats", "\n")
cat("\tget_controlled_list_phase_or_stage", "\n")
cat("\tget_controlled_list_sex", "\n")
cat("\tget_controlled_list_specimen_type_status", "\n")
cat("\tget_controlled_list_taxonomic_status", "\n")
cat("\tget_controlled_lists", "\n")
cat("\tget_rest_services", "\n")
cat("\tget_setting", "\n")
cat("\tget_settings", "\n")
cat("\tget_source_systems", "\n")
cat("\tping\n")
invisible(self)
}
)
)
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