R/TaxonClient.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 Taxon operations
#' @description This client connects to all Taxon-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 <- TaxonClient$new()
#'
#' @section Methods:
#' \describe{
#' \item{\code{ count }}{
#'
#' Get the number of taxa matching a given condition;
#' Conditions given as query parameters or a querySpec JSON.
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ integer }
#' }
#' \item{\code{ count_distinct_values }}{
#'
#' Count the distinct number of values that exist for a given field;
#' See also endpoint /getDistinctValues.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ field } : name of field in the taxon object
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ count_distinct_values_per_group }}{
#'
#' Count the distinct number of field values that exist per the given field to group by;
#' See also endpoint /getDistinctValuesPerGroup.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ group } : name of field in the taxon object you want to group by \item \code{ field } : name of field in the taxon object
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ download_query }}{
#'
#' Dynamic download service: Query for taxa and return result as a stream ...;
#' Query with query parameters or querySpec JSON. ....
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ Taxon }
#' }
#' \item{\code{ dwca_get_data_set }}{
#'
#' Download dataset as Darwin Core Archive File;
#' Available datasets can be queried with /taxon/dwca/getDataSetNames. Response saved to <datasetname>-<yyyymmdd>.dwca.zip.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ dataset } : name of dataset
#'
#' \item \code{ filename } : location to save data, defaults to \code{format(Sys.time(), "download-\%Y-\%m-\%dT\%H:\%m.zip")}
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ }
#' }
#' \item{\code{ dwca_get_data_set_names }}{
#'
#' Retrieve the names of all available datasets;
#' Individual datasets can then be downloaded with /dwca/getDataSet/{dataset}.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ dwca_query }}{
#'
#' Dynamic download service: Query for taxa and return result as Darwin Core Archive File;
#' Query with query parameters or querySpec JSON. Response saved to nba-taxa.dwca.zip.
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#' \item \code{ filename } : location to save data, defaults to \code{format(Sys.time(), "download-\%Y-\%m-\%dT\%H:\%m.zip")}
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ }
#' }
#' \item{\code{ find }}{
#'
#' Find a taxon by id;
#' If found, returns a single taxon.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ id } : id of taxon
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ Taxon }
#' }
#' \item{\code{ find_by_ids }}{
#'
#' Find taxa by ids;
#' Given multiple ids, returns a list of taxa.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ ids } : ids of multiple taxa, separated by comma
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ Taxon }
#' }
#' \item{\code{ get_distinct_values }}{
#'
#' Get all different values that can be found for one field;
#' A list of all fields for taxon documents can be retrieved with /metadata/getFieldInfo.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ field } : name of field in a taxon object
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_distinct_values_per_group }}{
#'
#' Get all distinct values (and their document count) for the field given divided per distinct value of the field to group by;
#' See also endpoint /getDistinctValues.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ group } : name of field in the taxon object you want to group by \item \code{ field } : name of field in the taxon object
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_field_info }}{
#'
#' Returns extended information for each field of a specimen document;
#' Info consists of whether the fields is indexed, the ElasticSearch datatype and a list of allowed operators.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_paths }}{
#'
#' Returns the full path of all fields within a document;
#' See also metadata/getFieldInfo for all allowed operators per field.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \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{ group_by_scientific_name }}{
#'
#' Aggregates Taxon and Specimen documents according to their scientific names;
#' Returns a list with ScientificNameGroups, which contain Taxon and Specimen documents that share a scientific name.
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ QueryResult }
#' }
#' \item{\code{ is_operator_allowed }}{
#'
#' Checks if a given operator is allowed for a given field;
#' See also metadata/getFieldInfo.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ field } : specimen document field \item \code{ operator } : operator
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ query }}{
#'
#' Query for taxa;
#' Search for taxa (GET) using query parameters or a querySpec JSON.
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ QueryResult }
#' }
#' }
#'
#' @export
TaxonClient <- R6::R6Class(
"TaxonClient",
inherit = ApiClient,
public = list(
initialize = function(basePath, userAgent) {
super$initialize(basePath, userAgent)
},
count = function(
querySpec = NULL,
queryParams = list(),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/count"
response <- self$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.integer(httr::content(response))
Response$new(result, response)
}
},
count_distinct_values = function(
field = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/countDistinctValues/{field}"
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, urlPath)
}
response <- self$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 a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
count_distinct_values_per_group = function(
group = NULL,
field = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/countDistinctValuesPerGroup/{group}/{field}"
if (!missing(`group`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "group", "\\}"), `group`, urlPath)
}
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, urlPath)
}
response <- self$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 a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
download_query = function(
querySpec = NULL,
queryParams = list(),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/download"
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$handleError(response)
} else {
## API call result is object of model class
returnObject <- Taxon$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)
}
},
dwca_get_data_set = function(
dataset = NULL,
filename = format(
Sys.time(),
"download-%Y-%m-%dT%H:%m.zip"
),
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/dwca/getDataSet/{dataset}"
if (!missing(`dataset`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "dataset", "\\}"), `dataset`, urlPath)
}
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
httr::write_disk(filename),
httr::progress(),
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
message("Query result written to ", filename)
## empty response, e.g. when file is downloaded
result <- NULL
Response$new(result, response)
}
},
dwca_get_data_set_names = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/dwca/getDataSetNames"
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)
}
},
dwca_query = function(
querySpec = NULL,
queryParams = list(),
filename = format(
Sys.time(),
"download-%Y-%m-%dT%H:%m.zip"
),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/dwca/query"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
httr::write_disk(filename),
httr::progress(),
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
message("Query result written to ", filename)
## empty response, e.g. when file is downloaded
result <- NULL
Response$new(result, response)
}
},
find = function(
id = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/find/{id}"
if (!missing(`id`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "id", "\\}"), `id`, urlPath)
}
response <- self$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 object of model class
returnObject <- Taxon$new()
## if API call result is QueryResult,
## list items must be mapped to model class
result <- returnObject$fromList(
httr::content(response),
typeMapping = list(item = private$getBaseDataType())
)
Response$new(result, response)
}
},
find_by_ids = function(
ids = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/findByIds/{ids}"
if (!missing(`ids`)) {
## build URL for path param
## input can be vector or string with comma separated items
## API takes string, so translate vector, if present
if (length(`ids`) > 1) {
ids <- paste(ids, collapse = ",")
}
urlPath <- gsub(paste0("\\{", "ids", "\\}"), `ids`, 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$handleError(response)
} else {
## API call result is object of model class
returnObject <- Taxon$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_distinct_values = function(
field = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/getDistinctValues/{field}"
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, 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$handleError(response)
} else {
## API call result is a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
get_distinct_values_per_group = function(
group = NULL,
field = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/getDistinctValuesPerGroup/{group}/{field}"
if (!missing(`group`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "group", "\\}"), `group`, urlPath)
}
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, 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_field_info = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/metadata/getFieldInfo"
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_paths = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/metadata/getPaths"
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_setting = function(
name = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/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 <- "/taxon/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)
}
},
group_by_scientific_name = function(
querySpec = NULL,
queryParams = list(),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/groupByScientificName"
response <- self$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 <- QueryResult$new()
## if API call result is QueryResult,
## list items must be mapped to model class
result <- returnObject$fromList(
httr::content(response),
typeMapping = list(item = private$getBaseDataType())
)
Response$new(result, response)
}
},
is_operator_allowed = function(
field = NULL,
operator = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/metadata/isOperatorAllowed/{field}/{operator}"
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, urlPath)
}
if (!missing(`operator`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "operator", "\\}"), `operator`, 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$handleError(response)
} else {
## API call result is a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
query = function(
querySpec = NULL,
queryParams = list(),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/query"
response <- self$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 <- QueryResult$new()
## if API call result is QueryResult,
## list items must be mapped to model class
result <- returnObject$fromList(
httr::content(response),
typeMapping = list(item = private$getBaseDataType())
)
Response$new(result, response)
}
},
print = function(...) {
## print class name
cat("<TaxonClient>\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("\tcount", "\n")
cat("\tcount_distinct_values", "\n")
cat("\tcount_distinct_values_per_group", "\n")
cat("\tdownload_query", "\n")
cat("\tdwca_get_data_set", "\n")
cat("\tdwca_get_data_set_names", "\n")
cat("\tdwca_query", "\n")
cat("\tfind", "\n")
cat("\tfind_by_ids", "\n")
cat("\tget_distinct_values", "\n")
cat("\tget_distinct_values_per_group", "\n")
cat("\tget_field_info", "\n")
cat("\tget_paths", "\n")
cat("\tget_setting", "\n")
cat("\tget_settings", "\n")
cat("\tgroup_by_scientific_name", "\n")
cat("\tis_operator_allowed", "\n")
cat("\tquery", "\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 Taxon operations
#' @description This client connects to all Taxon-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 <- TaxonClient$new()
#'
#' @section Methods:
#' \describe{
#' \item{\code{ count }}{
#'
#' Get the number of taxa matching a given condition;
#' Conditions given as query parameters or a querySpec JSON.
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ integer }
#' }
#' \item{\code{ count_distinct_values }}{
#'
#' Count the distinct number of values that exist for a given field;
#' See also endpoint /getDistinctValues.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ field } : name of field in the taxon object
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ count_distinct_values_per_group }}{
#'
#' Count the distinct number of field values that exist per the given field to group by;
#' See also endpoint /getDistinctValuesPerGroup.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ group } : name of field in the taxon object you want to group by \item \code{ field } : name of field in the taxon object
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ download_query }}{
#'
#' Dynamic download service: Query for taxa and return result as a stream ...;
#' Query with query parameters or querySpec JSON. ....
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ Taxon }
#' }
#' \item{\code{ dwca_get_data_set }}{
#'
#' Download dataset as Darwin Core Archive File;
#' Available datasets can be queried with /taxon/dwca/getDataSetNames. Response saved to <datasetname>-<yyyymmdd>.dwca.zip.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ dataset } : name of dataset
#'
#' \item \code{ filename } : location to save data, defaults to \code{format(Sys.time(), "download-\%Y-\%m-\%dT\%H:\%m.zip")}
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ }
#' }
#' \item{\code{ dwca_get_data_set_names }}{
#'
#' Retrieve the names of all available datasets;
#' Individual datasets can then be downloaded with /dwca/getDataSet/{dataset}.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \item{\code{ dwca_query }}{
#'
#' Dynamic download service: Query for taxa and return result as Darwin Core Archive File;
#' Query with query parameters or querySpec JSON. Response saved to nba-taxa.dwca.zip.
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#' \item \code{ filename } : location to save data, defaults to \code{format(Sys.time(), "download-\%Y-\%m-\%dT\%H:\%m.zip")}
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ }
#' }
#' \item{\code{ find }}{
#'
#' Find a taxon by id;
#' If found, returns a single taxon.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ id } : id of taxon
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ Taxon }
#' }
#' \item{\code{ find_by_ids }}{
#'
#' Find taxa by ids;
#' Given multiple ids, returns a list of taxa.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ ids } : ids of multiple taxa, separated by comma
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ Taxon }
#' }
#' \item{\code{ get_distinct_values }}{
#'
#' Get all different values that can be found for one field;
#' A list of all fields for taxon documents can be retrieved with /metadata/getFieldInfo.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ field } : name of field in a taxon object
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_distinct_values_per_group }}{
#'
#' Get all distinct values (and their document count) for the field given divided per distinct value of the field to group by;
#' See also endpoint /getDistinctValues.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ group } : name of field in the taxon object you want to group by \item \code{ field } : name of field in the taxon object
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_field_info }}{
#'
#' Returns extended information for each field of a specimen document;
#' Info consists of whether the fields is indexed, the ElasticSearch datatype and a list of allowed operators.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ get_paths }}{
#'
#' Returns the full path of all fields within a document;
#' See also metadata/getFieldInfo for all allowed operators per field.
#'
#' Parameters:
#' \itemize{
#'
#'
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ character }
#' }
#' \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{ group_by_scientific_name }}{
#'
#' Aggregates Taxon and Specimen documents according to their scientific names;
#' Returns a list with ScientificNameGroups, which contain Taxon and Specimen documents that share a scientific name.
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ QueryResult }
#' }
#' \item{\code{ is_operator_allowed }}{
#'
#' Checks if a given operator is allowed for a given field;
#' See also metadata/getFieldInfo.
#'
#' Parameters:
#' \itemize{
#'
#' \item \code{ field } : specimen document field \item \code{ operator } : operator
#'
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ list }
#' }
#' \item{\code{ query }}{
#'
#' Query for taxa;
#' Search for taxa (GET) using query parameters or a querySpec JSON.
#'
#' Parameters:
#' \itemize{
#' \item \code{ query_spec } : Object of type QuerySpec or its JSON representation
#'
#' \item \code{ queryParams } : named list or vector with query parameters
#'
#' \item \code{ ... } : additional parameters passed to httr::GET
#' }
#' Returns:
#' \code{ QueryResult }
#' }
#' }
#'
#' @export
TaxonClient <- R6::R6Class(
"TaxonClient",
inherit = ApiClient,
public = list(
initialize = function(basePath, userAgent) {
super$initialize(basePath, userAgent)
},
count = function(
querySpec = NULL,
queryParams = list(),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/count"
response <- self$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.integer(httr::content(response))
Response$new(result, response)
}
},
count_distinct_values = function(
field = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/countDistinctValues/{field}"
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, urlPath)
}
response <- self$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 a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
count_distinct_values_per_group = function(
group = NULL,
field = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/countDistinctValuesPerGroup/{group}/{field}"
if (!missing(`group`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "group", "\\}"), `group`, urlPath)
}
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, urlPath)
}
response <- self$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 a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
download_query = function(
querySpec = NULL,
queryParams = list(),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/download"
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$handleError(response)
} else {
## API call result is object of model class
returnObject <- Taxon$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)
}
},
dwca_get_data_set = function(
dataset = NULL,
filename = format(
Sys.time(),
"download-%Y-%m-%dT%H:%m.zip"
),
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/dwca/getDataSet/{dataset}"
if (!missing(`dataset`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "dataset", "\\}"), `dataset`, urlPath)
}
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
httr::write_disk(filename),
httr::progress(),
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
message("Query result written to ", filename)
## empty response, e.g. when file is downloaded
result <- NULL
Response$new(result, response)
}
},
dwca_get_data_set_names = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/dwca/getDataSetNames"
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)
}
},
dwca_query = function(
querySpec = NULL,
queryParams = list(),
filename = format(
Sys.time(),
"download-%Y-%m-%dT%H:%m.zip"
),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/dwca/query"
response <- self$callApi(
url = paste0(self$basePath, urlPath),
method = "GET",
queryParams = as.list(queryParams),
headerParams = headerParams,
body = body,
httr::write_disk(filename),
httr::progress(),
...
)
if (httr::status_code(response) < 200 ||
httr::status_code(response) > 299) {
self$handleError(response)
} else {
message("Query result written to ", filename)
## empty response, e.g. when file is downloaded
result <- NULL
Response$new(result, response)
}
},
find = function(
id = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/find/{id}"
if (!missing(`id`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "id", "\\}"), `id`, urlPath)
}
response <- self$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 object of model class
returnObject <- Taxon$new()
## if API call result is QueryResult,
## list items must be mapped to model class
result <- returnObject$fromList(
httr::content(response),
typeMapping = list(item = private$getBaseDataType())
)
Response$new(result, response)
}
},
find_by_ids = function(
ids = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/findByIds/{ids}"
if (!missing(`ids`)) {
## build URL for path param
## input can be vector or string with comma separated items
## API takes string, so translate vector, if present
if (length(`ids`) > 1) {
ids <- paste(ids, collapse = ",")
}
urlPath <- gsub(paste0("\\{", "ids", "\\}"), `ids`, 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$handleError(response)
} else {
## API call result is object of model class
returnObject <- Taxon$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_distinct_values = function(
field = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/getDistinctValues/{field}"
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, 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$handleError(response)
} else {
## API call result is a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
get_distinct_values_per_group = function(
group = NULL,
field = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/getDistinctValuesPerGroup/{group}/{field}"
if (!missing(`group`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "group", "\\}"), `group`, urlPath)
}
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, 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_field_info = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/metadata/getFieldInfo"
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_paths = function(
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/metadata/getPaths"
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_setting = function(
name = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/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 <- "/taxon/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)
}
},
group_by_scientific_name = function(
querySpec = NULL,
queryParams = list(),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/groupByScientificName"
response <- self$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 <- QueryResult$new()
## if API call result is QueryResult,
## list items must be mapped to model class
result <- returnObject$fromList(
httr::content(response),
typeMapping = list(item = private$getBaseDataType())
)
Response$new(result, response)
}
},
is_operator_allowed = function(
field = NULL,
operator = NULL,
...) {
headerParams <- character()
queryParams <- list()
urlPath <- "/taxon/metadata/isOperatorAllowed/{field}/{operator}"
if (!missing(`field`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "field", "\\}"), `field`, urlPath)
}
if (!missing(`operator`)) {
## build URL for path param
urlPath <- gsub(paste0("\\{", "operator", "\\}"), `operator`, 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$handleError(response)
} else {
## API call result is a "map container" and will be parsed to list
result <- httr::content(response, simplifyVector = TRUE)
Response$new(result, response)
}
},
query = function(
querySpec = NULL,
queryParams = list(),
...) {
headerParams <- character()
if (!is.null(querySpec) & length(queryParams) > 0) {
stop("Either querySpec or queryParams argument allowed, not both.")
}
if (!missing(`querySpec`)) {
## querySpec can be either JSON string or object of type QuerySpec.
param <- ifelse(typeof(`querySpec`) == "environment",
`querySpec`$toJSONString(),
`querySpec`
)
queryParams["querySpec"] <- param
}
## querySpec parameter has underscore in NBA, omitted in argument
names(queryParams) <- gsub(
"querySpec",
"_querySpec",
names(queryParams)
)
urlPath <- "/taxon/query"
response <- self$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 <- QueryResult$new()
## if API call result is QueryResult,
## list items must be mapped to model class
result <- returnObject$fromList(
httr::content(response),
typeMapping = list(item = private$getBaseDataType())
)
Response$new(result, response)
}
},
print = function(...) {
## print class name
cat("<TaxonClient>\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("\tcount", "\n")
cat("\tcount_distinct_values", "\n")
cat("\tcount_distinct_values_per_group", "\n")
cat("\tdownload_query", "\n")
cat("\tdwca_get_data_set", "\n")
cat("\tdwca_get_data_set_names", "\n")
cat("\tdwca_query", "\n")
cat("\tfind", "\n")
cat("\tfind_by_ids", "\n")
cat("\tget_distinct_values", "\n")
cat("\tget_distinct_values_per_group", "\n")
cat("\tget_field_info", "\n")
cat("\tget_paths", "\n")
cat("\tget_setting", "\n")
cat("\tget_settings", "\n")
cat("\tgroup_by_scientific_name", "\n")
cat("\tis_operator_allowed", "\n")
cat("\tquery", "\n")
cat("\tping\n")
invisible(self)
}
)
)
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