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api.R
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#* @apiTitle Finnish Biodiversity Indicators HTTP API
#* @apiTOS https://laji.fi/en/about/845
suppressPackageStartupMessages({
library(DBI, warn.conflicts = FALSE, quietly = TRUE)
library(dplyr, warn.conflicts = FALSE, quietly = TRUE)
library(fbi, warn.conflicts = FALSE, quietly = TRUE)
library(plumber, warn.conflicts = FALSE, quietly = TRUE)
library(pool, warn.conflicts = FALSE, quietly = TRUE)
library(rapidoc, warn.conflicts = FALSE, quietly = TRUE)
library(readr, warn.conflicts = FALSE, quietly = TRUE)
library(RPostgres, warn.conflicts = FALSE, quietly = TRUE)
})
Sys.setenv(R_CONFIG_FILE = "config.yml")
pool <- dbPool(Postgres())
tryCatch(
{
if (!"tablefunc" %in% pull(tbl(pool, "pg_extension"), extname)) {
dbExecute(pool, "CREATE EXTENSION tablefunc")
}
},
error = function(e) message(e[["message"]])
)
dir.create("var/logs", showWarnings = FALSE)
#* @filter cors
cors <- function(req, res) {
res[["setHeader"]]("Access-Control-Allow-Origin", "*")
if (req[["REQUEST_METHOD"]] == "OPTIONS") {
res[["setHeader"]]("Access-Control-Allow-Methods", "*")
res[["setHeader"]](
"Access-Control-Allow-Headers",
req[["HTTP_ACCESS_CONTROL_REQUEST_HEADERS"]]
)
res[["status"]] <- 200L
return(list())
} else {
plumber::forward()
}
}
#* @filter secret
function(req, res) {
secret <- identical(req[["argsQuery"]][["secret"]], Sys.getenv("JOB_SECRET"))
if (grepl("job", req[["PATH_INFO"]]) && !secret) {
res[["status"]] <- 401
list(error = "Access token required")
} else {
plumber::forward()
}
}
#* Register result of job
#* @tag status
#* @get /job
#* @response 200 A json object response
#* @serializer unboxedJSON
function(status) {
cat(status, file = "status/success.txt")
cat(format(Sys.time(), usetz = TRUE), file = "status/last-update.txt")
"success"
}
#* Register log of job
#* @tag status
#* @post /job-logs
#* @param file:file Log file.
#* @response 200 A json object response
#* @serializer unboxedJSON
function(file = "") {
log_file <- paste0("var/logs/", names(file)[[1L]])
writeBin(file[[1L]], log_file)
file.copy(log_file, "var/logs/update-latest.txt", TRUE)
"Job logged"
}
#* Check the liveness of the API
#* @tag status
#* @head /healthz
#* @get /healthz
#* @response 200 A json object response
#* @serializer unboxedJSON
function() {
""
}
#* Get list of available indicators
#* @tag lists
#* @get /indices
#* @response 200 A json array response
#* @serializer unboxedJSON
function() {
get_indices()
}
#* Get list of taxa available for an indicator
#* @tag lists
#* @get /taxa/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @response 200 A json array response
#* @response 404 Not Found
#* @serializer unboxedJSON
function(index, res) {
indices <- vapply(get_indices(), getElement, "", "code")
if (index %in% indices) {
ans <- config::get("taxa", config = index)
} else {
res[["status"]] <- 404L
return("Not found")
}
ans
}
#* Get list of taxa available for an indicator (but not included in multi-taxon indicator)
#* @tag lists
#* @get /taxa-extra/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @response 200 A json array response
#* @response 404 Not Found
#* @serializer unboxedJSON
function(index, res) {
indices <- vapply(get_indices(), getElement, "", "code")
if (index %in% indices) {
ans <- config::get("extra_taxa", config = index)
} else {
res[["status"]] <- 404L
return("Not found")
}
ans
}
#* Get the configuration for an indicator
#* @tag config
#* @get /config/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @response 200 A json array response
#* @response 404 Not Found
#* @serializer unboxedJSON
function(index, res) {
indices <- vapply(get_indices(), getElement, "", "code")
if (index %in% indices) {
ans <- config::get(config = index)
ans[["taxa"]] <- NULL
ans[["extra_taxa"]] <- NULL
if (hasName(ans, "from")) {
ans[["surveys"]] <- NULL
ans[["counts"]] <- NULL
ans[["filters"]] <- NULL
}
} else {
res[["status"]] <- 404L
return("Not found")
}
unclass(ans)
}
#* Get data for an indicator as JSON
#* @tag data
#* @get /data/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @param model:str Which model one of `trim`, `rbms`, etc. (`default` is first model declared in [configuration](#get-/config/-index- "Get the configuration of an indicator")).
#* @param taxon:str FinBIF MX code identifier for a taxon (see [/taxa](#get-/taxa/-index- "Get list of taxa available for an indicator") or [/taxa-extra](#get-/taxa-extra/-index- "Get list of extra taxa available for an indicator")).
#* @param region:str Which region: `north`, `south` or `none` (whole of Finland)?
#* @response 200 A json object response
#* @response 404 Not found
#* @serializer unboxedJSON
function(index, model = "default", taxon = "none", region = "none", res) {
has_output <- check_input(index, model, taxon)
if (!has_output || !region %in% c("none", "south", "north")) {
res[["status"]] <- 404L
return("Not found")
}
ans <- get_output("data", index, model, taxon, region, pool)
if (is.raw(ans)) {
ans <- unserialize(ans)
} else {
res[["status"]] <- 500L
}
ans
}
#* Get data for an indicator as CSV
#* @tag data
#* @get /csv/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @param model:str Which model one of `trim`, `rbms`, etc. (`default` is first model declared in [configuration](#get-/config/-index- "Get the configuration of an indicator")).
#* @param taxon:str FinBIF MX code identifier for a taxon (see [/taxa](#get-/taxa/-index- "Get list of taxa available for an indicator") or [/taxa-extra](#get-/taxa-extra/-index- "Get list of extra taxa available for an indicator")).
#* @param region:str Which region: `north`, `south` or `none` (whole of Finland)?
#* @response 200 A csv file response
#* @response 404 Not found
function(index, model = "default", taxon = "none", region = "none", res) {
has_output <- check_input(index, model, taxon)
if (!has_output || !region %in% c("none", "south", "north")) {
res[["serializer"]] <- plumber::serializer_unboxed_json()
res[["status"]] <- 404L
return("Not found")
}
ans <- get_output("data_csv", index, model, taxon, region, pool)
if (is.raw(ans)) {
res[["serializer"]] <- plumber::serializer_csv()
ans <- unserialize(ans)
} else {
res[["serializer"]] <- plumber::serializer_unboxed_json()
res[["status"]] <- 500L
}
ans
}
#* Get count summary for an indicator
#* @tag statistics
#* @get /count-summary/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @param model:str Which model one of `trim`, `rbms`, etc. (`default` is first model declared in [configuration](#get-/config/-index- "Get the configuration of an indicator")).
#* @param taxon:str FinBIF MX code identifier for a taxon (see [/taxa](#get-/taxa/-index- "Get list of taxa available for an indicator") or [/taxa-extra](#get-/taxa-extra/-index- "Get list of extra taxa available for an indicator")).
#* @param region:str Which region: `north`, `south` or `none` (whole of Finland)?
#* @response 200 A json object response
#* @response 404 Not found
#* @serializer unboxedJSON
function(index, model = "default", taxon = "none", region = "none", res) {
has_output <- check_input(index, model, taxon)
if (!has_output || !region %in% c("none", "south", "north")) {
res[["status"]] <- 404L
return("Not found")
}
ans <- get_output("count_summary", index, model, taxon, region, pool)
if (is.raw(ans)) {
ans <- unserialize(ans)
} else {
res[["status"]] <- 500L
}
ans
}
#* Get trend summary for an indicator
#* @tag statistics
#* @get /trends/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @param model:str Which model one of `trim`, `rbms`, etc. (`default` is first model declared in [configuration](#get-/config/-index- "Get the configuration of an indicator")).
#* @param taxon:str FinBIF MX code identifier for a taxon (see [/taxa](#get-/taxa/-index- "Get list of taxa available for an indicator") or [/taxa-extra](#get-/taxa-extra/-index- "Get list of extra taxa available for an indicator")).
#* @param region:str Which region: `north`, `south` or `none` (whole of Finland)?
#* @response 200 An json object response
#* @response 404 Not found
#* @serializer unboxedJSON
function(index, model = "default", taxon = "none", region = "none", res) {
has_output <- check_input(index, model, taxon)
if (!has_output || !region %in% c("none", "south", "north")) {
res[["status"]] <- 404L
return("Not found")
}
ans <- get_output("trends", index, model, taxon, region, pool)
if (is.raw(ans)) {
ans <- unserialize(ans)
} else {
res[["status"]] <- 500L
}
ans
}
#* Get a state or list of states for indicators
#* @tag statistics
#* @get /state/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @param model:str Which model one of `trim`, `rbms`, etc. (`default` is first model declared in [configuration](#get-/config/-index- "Get the configuration of an indicator")).
#* @param taxon:str FinBIF MX code identifier for a taxon (see [/taxa](#get-/taxa/-index- "Get list of taxa available for an indicator") or [/taxa-extra](#get-/taxa-extra/-index- "Get list of extra taxa available for an indicator")). Or `all` (for all taxa used by the multi-taxon index) or `extra` for all extra taxa.
#* @param region:str Which region: `north`, `south` or `none` (whole of Finland)?
#* @response 200 An json object response
#* @response 404 Not found
#* @serializer unboxedJSON
function(index, model = "default", taxon = "none", region = "none", res) {
has_output <- check_input(index, model, taxon)
if (!has_output || !region %in% c("none", "south", "north")) {
res[["status"]] <- 404L
return("Not found")
}
if (taxon == "all") {
taxa <- config::get("taxa", config = index)
taxa <- vapply(taxa, getElement, "", "code")
state <- vapply(
taxa,
\(x) get_output("model_state", index, model, x, region, pool)[[1L]],
""
)
ans <- data.frame(taxon = as.vector(taxa), state = as.vector(state))
} else if (taxon == "extra") {
taxa <- config::get("extra_taxa", config = index)
taxa <- vapply(taxa, getElement, "", "code")
state <- vapply(
taxa,
\(x) get_output("model_state", index, model, x, region, pool)[[1L]],
""
)
ans <- data.frame(taxon = as.vector(taxa), state = as.vector(state))
} else {
state <- get_output("model_state", index, model, taxon, region, pool)
ans <- data.frame(state = state)
}
ans
}
#* Get image for an indicator as SVG
#* @tag graphics
#* @get /svg/<index:str>
#* @param index:str Shortcode for multi-taxon indicator (see [/indices](#get-/indices "Get list of available indicators")).
#* @param model:str Which model one of `trim`, `rbms`, etc. (`default` is first model declared in [configuration](#get-/config/-index- "Get the configuration of an indicator")).
#* @param taxon:str FinBIF MX code identifier for a taxon (see [/taxa](#get-/taxa/-index- "Get list of taxa available for an indicator") or [/taxa-extra](#get-/taxa-extra/-index- "Get list of extra taxa available for an indicator")).
#* @param region:str Which region: `north`, `south` or `none` (whole of Finland)?
#* @param fontsize:double Font size (in px) of the axis labels.
#* @param scale:double Scale of image (%).
#* @response 200 An svg file response
#* @response 404 Not found
function(
index, model = "default", taxon = "none", region = "none", fontsize = 8.80,
scale = 100, res
) {
has_output <- check_input(index, model, taxon)
if (!has_output || !region %in% c("none", "south", "north")) {
res[["serializer"]] <- plumber::serializer_unboxed_json()
res[["status"]] <- 404L
return("Not found")
}
ans <- get_output("svg", index, model, taxon, region, pool)
if (is.raw(ans)) {
if (fontsize != 8.8 || scale != 100) {
con <- rawConnection(ans)
on.exit(close(con))
gcon <- gzcon(con)
ans <- readBin(gcon, "raw", n = 100000)
ans <- rawToChar(ans)
fontsize <- as.numeric(fontsize)
fontsize <- sprintf("font-size: %spx", fontsize)
ans <- gsub("font-size: 8\\.80px", fontsize, ans)
scale <- as.numeric(scale)
width <- sprintf("width=\"%spt\"", round(720 * scale / 100, 2))
height <- sprintf("height=\"%spt\"", round(576 * scale / 100, 2))
ans <- gsub("width='720\\.00pt'", width, ans)
ans <- gsub("height='576\\.00pt'", height, ans)
tmp <- tempfile(fileext = ".svgz")
writeLines(ans, tmp)
svglite::create_svgz(tmp)
ans <- readBin(tmp, "raw", n = file.info(tmp)[["size"]])
on.exit(unlink(tmp), add = TRUE)
}
res[["setHeader"]]("Content-Type", "image/svg+xml")
res[["setHeader"]]("Content-Encoding", "gzip")
res[["setHeader"]]("Content-Disposition", "inline")
res[["body"]] <- ans
res
} else {
res[["serializer"]] <- plumber::serializer_unboxed_json()
res[["status"]] <- 400L
ans
}
}
#* @assets ./var/logs /logs
list()
#* @assets ./status /status
list()
#* @assets /usr/local/lib/R/site-library/finbif/help/figures
list()
#* @get /favicon.ico
#* @serializer contentType list(type="image/x-icon")
function() {
readBin("favicon.ico", "raw", n = file.info("favicon.ico")$size)
}
#* @get /robots.txt
#* @serializer contentType list(type="text/plain")
function() {
readBin("robots.txt", "raw", n = file.info("robots.txt")$size)
}
#* @get /
function(res) {
path <- "/docs/index.html"
if (length(unlist(packageVersion("fbi"))) > 3L) {
path <- "/docs/dev/index.html"
}
res[["status"]] <- 303L
res[["setHeader"]]("Location", path)
}
#* @get /sitemap.xml
function(res) {
path <- "/docs/sitemap.xml"
if (length(unlist(packageVersion("fbi"))) > 3L) {
path <- "/docs/dev/sitemap.xml"
}
res[["status"]] <- 303L
res[["setHeader"]]("Location", path)
}
#* @get /pkgdown.yml
#* @serializer contentType list(type="text/yaml")
function(res) {
path <- "docs/pkgdown.yml"
if (length(unlist(packageVersion("fbi"))) > 3L) {
path <- "docs/dev/pkgdown.yml"
}
readBin(path, "raw", n = file.info(path)$size)
}
#* @get /docs/api.html
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/__docs__/")
}
#* @get /docs/dev/api.html
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/__docs__/")
}
#* @get /__docs__
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/__docs__/")
}
#* @get /docs/__docs__
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/__docs__/")
}
#* @get /docs/__docs__/
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/__docs__/")
}
#* @get /docs/dev/__docs__
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/__docs__/")
}
#* @get /docs/dev/__docs__/
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/__docs__/")
}
#* @get /docs
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/index.html")
}
#* @get /docs/
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/index.html")
}
#* @get /docs/dev
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/dev/index.html")
}
#* @get /docs/dev/
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/dev/index.html")
}
#* @get /docs/articles
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/articles/index.html")
}
#* @get /docs/dev/articles
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/dev/articles/index.html")
}
#* @get /docs/articles/
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/articles/index.html")
}
#* @get /docs/dev/articles/
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/dev/articles/index.html")
}
#* @get /docs/reference
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/reference/index.html")
}
#* @get /docs/dev/reference
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/dev/reference/index.html")
}
#* @get /docs/reference/
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/reference/index.html")
}
#* @get /docs/dev/reference/
function(res) {
res[["status"]] <- 303L
res[["setHeader"]]("Location", "/docs/dev/reference/index.html")
}
#* @assets ./docs /docs
list()
#* @plumber
function(pr) {
version <- as.character(utils::packageVersion("fbi"))
plumber::pr_set_api_spec(
pr,
function(spec) {
spec$info$version <- version
spec$info$description <- readChar("api.md", file.info("api.md")$size)
spec$info$contact$name <- "laji.fi support"
spec$info$contact$email <- "[email protected]"
spec$info$license$name <- "MIT"
spec$info$license$url <- "https://opensource.org/licenses/MIT"
spec$tags <- list(
list(
name = "lists",
description = "Endpoints to list available biodiversity indicators"
),
list(
name = "config",
description = paste(
"Endpoints to show how multi-taxon biodiversity indicators are",
"configured"
)
),
list(
name = "data",
description = "Endpoints to get biodiversity indicator output data"
),
list(
name = "statistics",
description = "Endpoints to get biodiversity indicator statistics"
),
list(
name = "graphics",
description = "Endpoints to get biodiversity indicator graphics"
)
)
spec$paths$`/healthz` <- NULL
spec$paths$`/job` <- NULL
spec$paths$`/job-logs` <- NULL
spec$paths$`/logs` <- NULL
spec$paths$`/favicon.ico` <- NULL
spec$paths$`/robots.txt` <- NULL
spec$paths$`/` <- NULL
spec$paths$`/sitemap.xml` <- NULL
spec$paths$`/docs/__docs__` <- NULL
spec$paths$`/docs/articles` <- NULL
spec$paths$`/docs/dev/articles` <- NULL
spec$paths$`/docs/reference` <- NULL
spec$paths$`/docs/dev/reference` <- NULL
spec$paths$`/__docs__` <- NULL
spec$paths$`/docs` <- NULL
spec$paths$`/docs/` <- NULL
spec$paths$`/docs/__docs__/` <- NULL
spec$paths$`/docs/articles/` <- NULL
spec$paths$`/docs/dev` <- NULL
spec$paths$`/docs/dev/` <- NULL
spec$paths$`/docs/dev/__docs__` <- NULL
spec$paths$`/docs/dev/__docs__/` <- NULL
spec$paths$`/docs/dev/articles/` <- NULL
spec$paths$`/docs/dev/reference/` <- NULL
spec$paths$`/docs/reference/` <- NULL
spec$paths$`/docs/api.html` <- NULL
spec$paths$`/docs/dev/api.html` <- NULL
spec$path$`/pkgdown.yml` <- NULL
set_description <- function(spec, path, description) {
spec$paths[[path]]$get$description <- description
spec
}
set_response_null <- function(spec, path) {
spec$paths[[path]]$get$responses$default <- NULL
spec$paths[[path]]$get$responses$`500`$content <- NULL
spec$paths[[path]]$get$responses$`404`$content <- NULL
spec
}
set_schema <- function(spec, path, resp, schema, example) {
content <- spec$paths[[path]]$get$responses[[resp]]$content
content$`application/json`$schema <- schema
content$`application/json`$example <- example
spec$paths[[path]]$get$responses[[resp]]$content <- content
spec
}
set_example <- function(spec, path, arg, example) {
spec$paths[[path]]$get$parameters[[arg]]$example <- example
spec
}
spec <- set_description(
spec,
"/indices",
paste(
"Gets a list of the available multi-taxon indicators. Returns both",
"indicator names and short-codes that can be used as indicator",
"identifiers for other endpoints."
)
)
spec <- set_response_null(spec, "/indices")
spec <- set_schema(
spec,
"/indices",
"200",
list(
type = "array",
items = list(
type = "object",
required = c("code", "name"),
properties = list(
code = list(
type = "string",
description = "Multi-taxon indicator shortcode."
),
name = list(
type = "string", description = "Multi-taxon indicator name."
)
)
)
),
data.frame(code = c("aa", "bb"), name = c("Indicator A", "Indicator B"))
)
spec <- set_description(
spec,
"/taxa/{index}",
paste(
"Gets the taxa that are available as single-taxon indices and that",
"are included in a given multi-taxon indicator. To list the",
"available indicators see [/indices](#get-/indices \"Get list of",
"available indicators\")."
)
)
spec <- set_example(spec, "/taxa/{index}", 1, "wb")
spec <- set_response_null(spec, "/taxa/{index}")
spec <- set_schema(
spec,
"/taxa/{index}",
"200",
list(
type = "array",
items = list(
type = "object",
required = c("code", "binomial"),
properties = list(
code = list(
type = "string",
description = "FinBIF taxon MX code identifier."
),
extra_codes = list(
type = "array",
description = paste(
"Extra FinBIF taxon MX code identifiers. These extra taxa",
"will also be included in the single-taxon indicator."
)
),
subtaxa = list(
type = "boolean",
description = paste(
"Whether the subtaxa of the taxa or extra taxa (see",
"extra_codes) are included in the single-taxon indicator."
)
),
binomial = list(
type = "string",
description = "Scientific name of the taxon."
),
start_year = list(
type = "integer",
description = paste(
"The taxon-specific base year for calucating relative",
"abundance."
)
),
sti = list(
type = "number",
description = "Species temperature index."
)
)
)
),
list(
list(
code = "MX.123",
extra_codes = c("MX.12", "MX.34"),
subtaxa = FALSE,
binomial = "Genus speciesa"
),
list(
code = "MX.456",
binomial = "Genus speicesb",
sti = 7.1
)
)
)
spec <- set_description(
spec,
"/taxa-extra/{index}",
paste(
"Gets the taxa that are available as single-taxon indices but",
"are not included in a given multi-taxon indicator. To list the",
"available indicators see",
"[/indices](#get-/indices \"Get list of available indicators\")."
)
)
spec <- set_example(spec, "/taxa-extra/{index}", 1, "wb")
spec <- set_response_null(spec, "/taxa-extra/{index}")
spec <- set_schema(
spec,
"/taxa-extra/{index}",
"200",
list(
type = "array",
items = list(
type = "object",
required = c("code", "binomial"),
properties = list(
code = list(
type = "string",
description = "FinBIF taxon MX code identifier."
),
extra_codes = list(
type = "array",
description = paste(
"Extra FinBIF taxon MX code identifiers. These extra taxa",
"will also be included in the single-taxon indicator."
)
),
subtaxa = list(
type = "boolean",
description = paste(
"Whether the subtaxa of the taxa or extra taxa (see",
"extra_codes) are included in the single-taxon indicator."
)
),
binomial = list(
type = "string",
description = "Scientific name of the taxon."
),
start_year = list(
type = "integer",
description = paste(
"The taxon-specific base year for calucating relative",
"abundance."
)
),