diff --git a/bin/export.r b/bin/export.r
new file mode 100755
index 0000000000000000000000000000000000000000..1fdc4f3a5137d1634c944cf2594178fdc210b934
--- /dev/null
+++ b/bin/export.r
@@ -0,0 +1,160 @@
+#!/usr/bin/Rscript --vanilla --no-save --no-restore --quiet --encoding=UTF-8
+# Call SIDO web service to get data
+#
+## Uses
+## - RCurl: https://cran.r-project.org/web/packages/RCurl/index.html
+## - keyring: https://cran.r-project.org/web/packages/keyring/index.html
+## - logger: https://cran.r-project.org/web/packages/logger/index.html
+
+sido_ws_url <- "https://sido.pheno.fr/ws"
+observatory_schema <- "foret"
+keyring_service <- "sido-export"
+
+#' Load or install a package.
+#'
+#' @param packagename string package name
+require_install_package <- function(packagename) {
+ if (!library(packagename, character.only=TRUE, logical.return=TRUE)) {
+ logger::log_info("Installing the library {packagename}...")
+ install.packages(packagename, repos = "http://cran.at.r-project.org/")
+ if (!library(packagename, character.only=TRUE, logical.return=TRUE)) {
+ logger::log_error("Installing the library {packagename} failed.")
+ q()
+ }
+ }
+ require(packagename, quietly = TRUE, character.only = TRUE)
+}
+
+require_install_package("RCurl")
+require_install_package("jsonlite")
+require_install_package("keyring")
+require_install_package("logger")
+
+#' Get keyring
+#'
+#' @return keyring for the script
+get_keyring <- function(keyring_service) {
+ logger::log_info("Using backend_file")
+ kr <- keyring::default_backend(keyring = keyring_service)
+ if (kr$keyring_is_locked(keyring=keyring_service)) {
+ kr$keyring_unlock(keyring = keyring_service)
+ }
+ kr
+}
+
+#' Get key value from keyring.
+#'
+#' @param kr keyring for the script
+#' @param key_name string key name
+#' @param prompt string prompt message
+#' @return string keyring value
+get_keyring_value <- function(kr, key_name, prompt) {
+ logger::log_info("Getting keyring value for {key_name}...")
+ if (!keyring::has_keyring_support()) {
+ logger::log_error("No keyring support!")
+ logger::log_info("Set value for the variable sido_{key_name} in the code.")
+ q()
+ }
+ keyring_service <- kr$keyring_default()
+
+ key_list <- kr$list()
+ match_keys <- subset(key_list,
+ service == keyring_service & username == key_name)
+ if (dim(match_keys)[1] == 0) {
+ logger::log_info("No value found for {keyring_service} and {key_name}.")
+ kr$set(service = keyring_service, username = key_name, prompt = prompt)
+ }
+ kr$get(service = keyring_service, username = key_name)
+}
+
+#' Get access token using client credentials.
+#'
+#' @param sido_url string root URL of SIDO WS
+#' @param sido_client_id string OAuth2 client ID for SIDO
+#' @param sido_client_secret string OAuth2 client secret for SIDO
+#' @return access token
+get_access_token <- function(sido_url, sido_client_id, sido_client_secret) {
+ logger::log_info("Getting access token...")
+ token_url <- paste0(sido_url, "/oauth/token")
+ # Perform the POST request
+ post_data <- paste0(
+ "client_id=", sido_client_id,
+ "&client_secret=", sido_client_secret,
+ "&grant_type=client_credentials")
+ headers <- c("Content-Type" = "application/x-www-form-urlencoded")
+ opts <- list(postfields = post_data, httpheader = headers)
+ logger::log_info("Calling {token_url}...")
+ post_response <- RCurl::postForm(token_url, .opts = opts)
+ logger::log_info("Parsing JSON...")
+ token <- jsonlite::fromJSON(post_response)
+ token$access_token
+}
+
+#' Get queries for a given schema.
+#'
+#' @param sido_url string root URL of SIDO WS
+#' @param schema string schema name
+#' @param access_token string access token
+#' @return queries list of query names
+get_queries <- function(sido_url, schema, access_token) {
+ logger::log_info("Getting queries...")
+ queries_url <- paste0(sido_url, "/data/queries/", schema)
+ headers <- c("Authorization" = paste0("Bearer ", access_token))
+ queries_response <- RCurl::getURL(queries_url,
+ .opts = list(httpheader = headers))
+ queries <- jsonlite::fromJSON(queries_response)
+ queries$data[, "name"]
+}
+
+#' Get data for a given schema and query.
+#'
+#' @param sido_url string root URL of SIDO WS
+#' @param schema string schema name
+#' @param query string query name
+#' @param access_token string access token
+#' @return data data frame
+get_data <- function(sido_url, schema, query, access_token) {
+ logger::log_info("- Getting data for {schema}/{query}...")
+ data_url <- paste0(sido_url, "/data/", schema, "/", query)
+ headers <- c("Authorization" = paste0("Bearer ", access_token))
+ data_response <- RCurl::getURL(data_url,
+ .opts = list(httpheader = headers),
+ .encoding = "UTF-8")
+ data <- jsonlite::fromJSON(data_response)
+ if (data$status != 200) {
+ logger::log_error(paste0(" Error ", data$status, ": ", data$message))
+ }
+ df <- data.frame(data$data$values)
+ names(df) <- data$data$properties$title
+ df
+}
+
+# Run
+
+kr <- get_keyring(keyring_service)
+sido_client_id <- get_keyring_value(kr, "client_id",
+ "Type your client_id for SIDO")
+sido_client_secret <- get_keyring_value(kr, "client_secret",
+ "Type your client_secret for SIDO")
+
+token <- get_access_token(sido_ws_url, sido_client_id, sido_client_secret)
+queries <- get_queries(sido_ws_url, observatory_schema, token)
+logger::log_info("- nb of queries: {0}", length(queries))
+for (i in seq_along(queries)) {
+ query = queries[i]
+ logger::log_info("- query: {query}")
+ if (query == "data") {
+ logger::log_info(" - skipping data query")
+ } else {
+ data <- get_data(sido_ws_url, observatory_schema, query, token)
+ filename <- paste0(observatory_schema, "-", query, ".csv")
+ logger::log_info(" - file: {filename}...")
+ write.table(data,
+ file = filename,
+ col.names = TRUE,
+ row.names = FALSE,
+ sep = ",",
+ quote = TRUE)
+ logger::log_info(" done")
+ }
+}
diff --git a/sido-gwt/src/main/java/fr/soeretempo/sido/gwt/server/ws/QueryServiceImpl.java b/sido-gwt/src/main/java/fr/soeretempo/sido/gwt/server/ws/QueryServiceImpl.java
index 73619af3687156e566903223dfb120be42ac59c0..b18d308c8f4d3357c0a6902f12894c3307b43b42 100644
--- a/sido-gwt/src/main/java/fr/soeretempo/sido/gwt/server/ws/QueryServiceImpl.java
+++ b/sido-gwt/src/main/java/fr/soeretempo/sido/gwt/server/ws/QueryServiceImpl.java
@@ -112,12 +112,15 @@ public class QueryServiceImpl implements QueryService {
@Override
public final WsQuery getQuery(@NonNull final Datasource obs,
- final String queryName) {
- if (getQueries(obs) != null) {
- return getQueries(obs).get(0);
- } else {
- return null;
+ @NonNull final String queryName) {
+ final var queries = getQueries(obs);
+ if (queries != null) {
+ return queries.stream()
+ .filter(query -> queryName.equals(query.getName()))
+ .findFirst()
+ .orElse(null);
}
+ return null;
}
@Override