Add regression tests for script helpers

R/getAllFromCoord.R

@@ -0,0 +1,57 @@
+combine_station_payloads <- function(station_payloads, station_lookup) {
+  station_payloads <- Filter(function(x) !is.null(x) && nrow(x), station_payloads)
+  if (!length(station_payloads)) {
+    return(NULL)
+  }
+
+  combined <- do.call("rbind.data.frame", station_payloads)
+  station_column <- c("POSTE", "geo_id_insee")
+  station_column <- station_column[station_column %in% names(combined)][1]
+
+  if (is.na(station_column)) {
+    return(combined)
+  }
+
+  combined$Nom_usuel <- unname(station_lookup[as.character(combined[[station_column]])])
+  combined
+}
+
+# Define function
+getAllFromCoord <- function(coord, start_date, end_date, allstations, N = 3, headers, base = "https://public-api.meteofrance.fr",btw_station_sleep = 1, within_statio_sleep=5,endpoint="public/DPClim/v1/") {
+  three_station = getIdFromCoords(coord, allstations, N = N)
+  alldata = lapply(three_station$Id_station, function(statid) {
+    print(paste("recuperer station", statid))
+    allstat = tryCatch(
+       getStationData(start_date = start_date, end_date = end_date, station_id = statid, headers = headers, base = base, timesleep=within_statio_sleep,dpclim=endpoint),
+       error = function(e) {print(e); NULL}
+    )
+    print(paste("done, sleep",btw_station_sleep,"sec"))
+    print(dim(allstat))
+    Sys.sleep(btw_station_sleep)
+    return(allstat)
+  })
+
+  ids = three_station$Nom_usuel
+  names(ids) = three_station$Id_station
+  combine_station_payloads(alldata, ids)
+}
+
+# Define function
+getAllFromCoordDPObs <- function(coord, start_date, end_date, allstations, N = 3, headers, base = "https://public-api.meteofrance.fr",btw_station_sleep = 1, within_statio_sleep=5,endpoint="public/DPClim/v1/") {
+  three_station = getIdFromCoords(coord, allstations, N = N)
+  alldata = lapply(three_station$Id_station, function(statid) {
+    print(paste("recuperer station", statid))
+    allstat = tryCatch(
+       getStationDataDPObs(start_date = start_date, end_date = end_date, station_id = statid, headers = headers, base = base, timesleep=within_statio_sleep,dpclim=endpoint),
+       error = function(e) {print(e); NULL}
+    )
+    print(paste("done, sleep",btw_station_sleep,"sec"))
+    print(dim(allstat))
+    Sys.sleep(btw_station_sleep)
+    return(allstat)
+  })
+
+  ids = three_station$Nom_usuel
+  names(ids) = three_station$Id_station
+  combine_station_payloads(alldata, ids)
+}

R/getStationData.R

@@ -1,7 +1,7 @@
 getStationData <- function(start_date, end_date, station_id,headers ,dpclim = "public/DPClim/v1/",timesleep=5,base="https://public-api.meteofrance.fr") {
     start_date <- as.Date(start_date)
     end_date <- as.Date(end_date)
-    url <- modify_url(base,path = paste0(dpclim,"commande-station/infrahoraire-6m"))
+    url <- httr::modify_url(base,path = paste0(dpclim,"commande-station/infrahoraire-6m"))
     # Format dates in ISO8601 format
     formatted_start_date <- format(start_date, "%Y-%m-%dT00:00:00Z", tz = "GMT")
     formatted_end_date <- format(end_date, "%Y-%m-%dT00:00:00Z", tz = "GMT")
@@ -9,31 +9,34 @@ getStationData <- function(start_date, end_date, station_id,headers ,dpclim = "p
     parameters <- list("id-station" = station_id, "date-deb-periode" = formatted_start_date, "date-fin-periode" = formatted_end_date)
 
     # Create the URL with parameters to ask for the csv file
-    url_query_file <- modify_url(url, query = parameters)
+    url_query_file <- httr::modify_url(url, query = parameters)
     response <- request_api(url_query_file, headers=headers,code=202)
-    if(response$status_code == 202){
-        url_fichier <- modify_url(base,path = paste0(dpclim,"commande/fichier"))
-        parameters <- list("id-cmde" = content(response)[[1]][[1]] )
+    if(!is.null(response) && response$status_code == 202){
+        url_fichier <- httr::modify_url(base,path = paste0(dpclim,"commande/fichier"))
+        parameters <- list("id-cmde" = httr::content(response)[[1]][[1]] )
         print(paste("Waiting for file",parameters[["id-cmde"]],"wait",timesleep,"secs"))
         Sys.sleep(timesleep)
-        url_get_file <- modify_url(url_fichier, query = parameters)
+        url_get_file <- httr::modify_url(url_fichier, query = parameters)
         response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
-        while(response$status_code %in% c(204,500)){
+        while(!is.null(response) && response$status_code %in% c(204,500)){
             print("file not ready yet, wait a minute more")
             Sys.sleep(60)
             response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
-            if(response$status_code == 500){
+            if(!is.null(response) && response$status_code == 500){
                 print("problem with file generation, retry")
                 response <- request_api(url_query_file, headers=headers,code=202)
-                parameters <- list("id-cmde" = content(response)[[1]][[1]] )
+                if (is.null(response)) {
+                    break
+                }
+                parameters <- list("id-cmde" = httr::content(response)[[1]][[1]] )
                 print(paste("Waiting for file",parameters[["id-cmde"]],"wait 25 sec"))
                 Sys.sleep(25)
-                url_get_file <- modify_url(url_fichier, query = parameters)
+                url_get_file <- httr::modify_url(url_fichier, query = parameters)
                 response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
             }
         }
-        if(response$status_code == 201){
-            return(read.csv(text=content(response,as="text")[[1]],sep=";",header=T,dec = ","))
+        if(!is.null(response) && response$status_code == 201){
+            return(read.csv(text=httr::content(response,as="text")[[1]],sep=";",header=T,dec = ","))
         }
     }
     print("Failed to retrieve data from the API. Why? not sure..")
@@ -44,7 +47,7 @@ getStationData <- function(start_date, end_date, station_id,headers ,dpclim = "p
 getStationDataDPObs <- function(start_date, end_date, station_id,headers ,dpclim = "public/DPClim/v1/",timesleep=5,base="https://public-api.meteofrance.fr") {
     start_date <- as.Date(start_date)
     end_date <- as.Date(end_date)
-    url <- modify_url(base,path = paste0(dpclim,"commande-station/infrahoraire-6m"))
+    url <- httr::modify_url(base,path = paste0(dpclim,"commande-station/infrahoraire-6m"))
     # Format dates in ISO8601 format
     formatted_start_date <- format(start_date, "%Y-%m-%dT00:00:00Z", tz = "GMT")
     formatted_end_date <- format(end_date, "%Y-%m-%dT00:00:00Z", tz = "GMT")
@@ -52,31 +55,34 @@ getStationDataDPObs <- function(start_date, end_date, station_id,headers ,dpclim
     parameters <- list("id-station" = station_id, "date-deb-periode" = formatted_start_date, "date-fin-periode" = formatted_end_date)
 
     # Create the URL with parameters to ask for the csv file
-    url_query_file <- modify_url(url, query = parameters)
+    url_query_file <- httr::modify_url(url, query = parameters)
     response <- request_api(url_query_file, headers=headers,code=202)
-    if(response$status_code == 202){
-        url_fichier <- modify_url(base,path = paste0(dpclim,"commande/fichier"))
-        parameters <- list("id-cmde" = content(response)[[1]][[1]] )
+    if(!is.null(response) && response$status_code == 202){
+        url_fichier <- httr::modify_url(base,path = paste0(dpclim,"commande/fichier"))
+        parameters <- list("id-cmde" = httr::content(response)[[1]][[1]] )
         print(paste("Waiting for file",parameters[["id-cmde"]],"wait",timesleep,"secs"))
         Sys.sleep(timesleep)
-        url_get_file <- modify_url(url_fichier, query = parameters)
+        url_get_file <- httr::modify_url(url_fichier, query = parameters)
         response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
-        while(response$status_code %in% c(204,500)){
+        while(!is.null(response) && response$status_code %in% c(204,500)){
             print("file not ready yet, wait a minute more")
             Sys.sleep(60)
             response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
-            if(response$status_code == 500){
+            if(!is.null(response) && response$status_code == 500){
                 print("problem with file generation, retry")
                 response <- request_api(url_query_file, headers=headers,code=202)
-                parameters <- list("id-cmde" = content(response)[[1]][[1]] )
+                if (is.null(response)) {
+                    break
+                }
+                parameters <- list("id-cmde" = httr::content(response)[[1]][[1]] )
                 print(paste("Waiting for file",parameters[["id-cmde"]],"wait 25 sec"))
                 Sys.sleep(25)
-                url_get_file <- modify_url(url_fichier, query = parameters)
+                url_get_file <- httr::modify_url(url_fichier, query = parameters)
                 response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
             }
         }
-        if(response$status_code == 201){
-            return(read.csv(text=content(response,as="text")[[1]],sep=";",header=T,dec = ","))
+        if(!is.null(response) && response$status_code == 201){
+            return(read.csv(text=httr::content(response,as="text")[[1]],sep=";",header=T,dec = ","))
         }
     }
     print("Failed to retrieve data from the API. Why? not sure..")
@@ -86,7 +92,7 @@ getStationDataDPObs <- function(start_date, end_date, station_id,headers ,dpclim
 getStationDataTemp <- function(start_date, end_date, station_id,headers ,dpclim = "public/DPClim/v1/",timesleep=5,base="https://public-api.meteofrance.fr") {
     start_date <- as.Date(start_date)
     end_date <- as.Date(end_date)
-    url <- modify_url(base,path = paste0(dpclim,"commande-station/infrahoraire-6m"))
+    url <- httr::modify_url(base,path = paste0(dpclim,"commande-station/infrahoraire-6m"))
     # Format dates in ISO8601 format
     formatted_start_date <- format(start_date, "%Y-%m-%dT00:00:00Z", tz = "GMT")
     formatted_end_date <- format(end_date, "%Y-%m-%dT00:00:00Z", tz = "GMT")
@@ -94,31 +100,34 @@ getStationDataTemp <- function(start_date, end_date, station_id,headers ,dpclim
     parameters <- list("id-station" = station_id, "date-deb-periode" = formatted_start_date, "date-fin-periode" = formatted_end_date)
 
     # Create the URL with parameters to ask for the csv file
-    url_query_file <- modify_url(url, query = parameters)
+    url_query_file <- httr::modify_url(url, query = parameters)
     response <- request_api(url_query_file, headers=headers,code=202)
-    if(response$status_code == 202){
-        url_fichier <- modify_url(base,path = paste0(dpclim,"commande/fichier"))
-        parameters <- list("id-cmde" = content(response)[[1]][[1]] )
+    if(!is.null(response) && response$status_code == 202){
+        url_fichier <- httr::modify_url(base,path = paste0(dpclim,"commande/fichier"))
+        parameters <- list("id-cmde" = httr::content(response)[[1]][[1]] )
         print(paste("Waiting for file",parameters[["id-cmde"]],"wait",timesleep,"secs"))
         Sys.sleep(timesleep)
-        url_get_file <- modify_url(url_fichier, query = parameters)
+        url_get_file <- httr::modify_url(url_fichier, query = parameters)
         response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
-        while(response$status_code %in% c(204,500)){
+        while(!is.null(response) && response$status_code %in% c(204,500)){
             print("file not ready yet, wait a minute more")
             Sys.sleep(60)
             response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
-            if(response$status_code == 500){
+            if(!is.null(response) && response$status_code == 500){
                 print("problem with file generation, retry")
                 response <- request_api(url_query_file, headers=headers,code=202)
-                parameters <- list("id-cmde" = content(response)[[1]][[1]] )
+                if (is.null(response)) {
+                    break
+                }
+                parameters <- list("id-cmde" = httr::content(response)[[1]][[1]] )
                 print(paste("Waiting for file",parameters[["id-cmde"]],"wait 25 sec"))
                 Sys.sleep(25)
-                url_get_file <- modify_url(url_fichier, query = parameters)
+                url_get_file <- httr::modify_url(url_fichier, query = parameters)
                 response <- request_api(url_get_file, headers=headers,code=c(204,201,500))
             }
         }
-        if(response$status_code == 201){
-            return(read.csv(text=content(response,as="text")[[1]],sep=";",header=T,dec = ","))
+        if(!is.null(response) && response$status_code == 201){
+            return(read.csv(text=httr::content(response,as="text")[[1]],sep=";",header=T,dec = ","))
         }
     }
     print("Failed to retrieve data from the API. Why? not sure..")
@@ -129,7 +138,7 @@ getStationDataTemp <- function(start_date, end_date, station_id,headers ,dpclim
 getStationDataDPObs <- function(start_date, end_date, station_id,headers ,dpclim = "public/DPObs/v1/",timesleep=5,base="https://public-api.meteofrance.fr") {
     start_date <- as.Date(start_date)
     end_date <- as.Date(end_date)
-    url <- modify_url(base,path = paste0(dpclim,"station/infrahoraire-6m"))
+    url <- httr::modify_url(base,path = paste0(dpclim,"station/infrahoraire-6m"))
     # Format dates in ISO8601 format
     formatted_start_date <- format(start_date, "%Y-%m-%dT12:00:00Z", tz = "GMT")
     formatted_end_date <- format(end_date, "%Y-%m-%dT00:00:00Z", tz = "GMT")
@@ -137,7 +146,7 @@ getStationDataDPObs <- function(start_date, end_date, station_id,headers ,dpclim
     parameters <- list("id_station" = station_id, "date" = formatted_start_date,'format'='csv')
 
     # Create the URL with parameters to ask for the csv file
-    url_query_file <- modify_url(url, query = parameters)
+    url_query_file <- httr::modify_url(url, query = parameters)
     response <- request_api(url_query_file, headers=headers,code=200)
     print(response)
     #if(response$status_code == 202){
@@ -168,4 +177,3 @@ getStationDataDPObs <- function(start_date, end_date, station_id,headers ,dpclim
     #print("Failed to retrieve data from the API. Why? not sure..")
 	#return(NULL)
 }
-

R/getStationInfo.R

@@ -1,14 +1,13 @@
 getStationInfo <- function(station, headers,infostat  = "information-station",dpclim = "public/DPClim/v1/") {
   # Assuming 'base' and 'dpclim' are defined externally; include 'infostat' parameter appropriately
-  url <- modify_url(base, path = paste0(dpclim, infostat), query = list("id-station" = station))
-  response <- GET(url,  headers)
+  url <- httr::modify_url(base, path = paste0(dpclim, infostat), query = list("id-station" = station))
+  response <- httr::GET(url,  headers)
   # Check if the request was successful
-  if (http_status(response)$category == "Success") {  # Ensure 'success' is lowercase as typically returned by the http_status() function
+  if (httr::http_status(response)$category == "Success") {
     # Properly parsing the content as CSV by directly reading the response text
-    data <- read.csv(text = content(response, as = "text"), sep = ";", header = TRUE)
+    data <- read.csv(text = httr::content(response, as = "text"), sep = ";", header = TRUE)
     return(data)  
   } 
   stop(sprintf("Failed to get station info  from the API. Status code: %s", response$status_code))
 }
 
-

R/getStationPaquet.R

@@ -1,15 +1,31 @@
-getStationPaquet <- function(id_station, format = "csv", headers = headersPaquet) {
-  base_url <- modify_url(base, path = paste0(dpPaquetObs, "infrahoraire-6m"))
-  url_with_params <- modify_url(base_url, query = list(id_station = id_station, format = format))
+getStationPaquet <- function(
+  id_station,
+  format = "csv",
+  headers,
+  endpoint = paste0(dpPaquetObs, "infrahoraire-6m")
+) {
+  url_with_params <- httr::modify_url(
+    base,
+    path = endpoint,
+    query = list(id_station = id_station, format = format)
+  )
 
-  response <- GET(url_with_params, add_headers(.headers = headers))
+  response <- request_api(
+    url_with_params = url_with_params,
+    headers = headers,
+    code = 200,
+    retry_limit = 3,
+    timesleep = 5
+  )
 
-  if (response$status_code == 200) {
-    # Successfully retrieved the data
-    return(read.csv(text = content(response, "text"), sep = ";", header = TRUE))
-  } else {
-    # If the request failed, it's useful to provide the status code in the error message for debugging
-    stop(sprintf("Failed to retrieve data as paquet from the API. Status code: %s", response$status_code))
+  if (is.null(response)) {
+    return(NULL)
   }
-}
 
+  read.csv(
+    text = httr::content(response, "text", encoding = "UTF-8"),
+    sep = ";",
+    header = TRUE,
+    stringsAsFactors = FALSE
+  )
+}

R/getStationsList.R

@@ -1,11 +1,11 @@
 getStations <- function(headers = headers,dpobs = "public/DPObs/v1/") {
   # Ensure dpobs is defined externally or provide a default/argument for it
-  url <- modify_url(base, path = paste0(dpobs, "liste-stations"))
-  response <- GET(url, add_headers(.headers = headers))
+  url <- httr::modify_url(base, path = paste0(dpobs, "liste-stations"))
+  response <- httr::GET(url, httr::add_headers(.headers = headers))
   # Better error handling
-  if (http_status(response)$category == "success") {
+  if (httr::http_status(response)$category == "Success") {
     # Directly parse the content as a CSV
-    data <- content(response, as = "text")
+    data <- httr::content(response, as = "text")
     # Return the data frame
     return(read.csv(text = data, sep = ";", header = TRUE))
   } else {
@@ -16,4 +16,3 @@ getStations <- function(headers = headers,dpobs = "public/DPObs/v1/") {
   }
 }
 
-

R/request.R

@@ -29,7 +29,7 @@ request_api <- function(url_with_params,headers,code,retry_limit=5,timesleep=20)
     success <- FALSE
 
     while(retry_count < retry_limit && !success) {
-        response <- tryCatch(GET(url_with_params, headers),error=function(e){print(e);NULL})
+        response <- tryCatch(httr::GET(url_with_params, headers),error=function(e){print(e);NULL})
         print(response)
         if(!is.null(response) && (response$status_code %in% code)) {
             success <- TRUE
@@ -37,11 +37,10 @@ request_api <- function(url_with_params,headers,code,retry_limit=5,timesleep=20)
             print(url_with_params)
             print(paste0("retry #",retry_count,"/",retry_limit))
             retry_count <- retry_count + 1
-            Sys.sleep(timesleep) 
+            Sys.sleep(timesleep*(1+retry_count/retry_limit))
         }
     }
     if(!success) return(NULL)
     else return(response)
 
 }
-

app.R

@@ -0,0 +1,96 @@
+# Load necessary libraries
+library(shiny)
+library(jsonlite)
+library(httr)
+library(shinycssloaders) # For the spinner
+
+# Assuming you have your custom functions in a file called 'your_functions.R'
+
+# List all R files in the directory and source them
+
+
+lapply(list.files(path = "R", pattern = "\\.R$", full.names = T), source)
+
+source("data/secrets")
+
+# Create a Bearer token header
+headers.default <- add_headers(
+  accept = "*/*",
+  apikey = token4
+)
+
+# Load station data
+
+# Define UI for application
+ui <- fluidPage(
+  tags$head(
+    tags$style(HTML("
+      #main {
+        height: 100vh; /* Full height of the viewport */
+        overflow-y: auto; /* Scroll if content overflows */
+      }
+      .container-fluid {
+        height: 100vh; /* Full height of the viewport */
+        display: flex;
+        flex-direction: column;
+      }
+      .row {
+        flex-grow: 1;
+        display: flex;
+      }
+      .col-sm-8 {
+        flex-grow: 1; /* Allow the main panel to grow */
+      }
+    "))
+  ),
+  
+  # Application title
+  titlePanel("Beaumont aka SECMONT"),
+  
+  # Sidebar for user inputs
+  sidebarLayout(
+    sidebarPanel(
+      width=2,
+      numericInput(inputId = "daysBefore", label = "Nb jour à  check:", value=10, min=1)
+    ),
+    
+    # Main panel for displaying plot
+    mainPanel(
+     width = 6,
+     withSpinner( plotOutput("dataPlot"))
+    )
+  )
+)
+
+# Define server logic required to generate and plot data
+server <- function(input, output) {
+  # Reactive expression to fetch data based on input and display spinner while loading
+  
+  
+  # Render the plot
+  output$dataPlot <- renderPlot({
+    startdate <- format(Sys.Date() - input$daysBefore, "%Y-%m-%d")
+    vignass.coor=c(44.8550665,5.8441789)
+    allstations <- read.csv("data/allstations.csv")
+    test1 <- getAllFromCoord(vignass.coor, start_date = startdate, end_date = format(Sys.Date(), "%Y-%m-%d"), allstations, headers = headers.default,btw_station_sleep = .5,within_statio_sleep = 1)
+    
+    # Prepare colors
+    cols <- palette.colors()[1:length(unique(test1$Nom_usuel))]
+    names(cols) <- unique(test1$Nom_usuel)
+    
+    # Filter data
+    testsep <- test1
+    testsep[testsep[,3] == 0 & !is.na(testsep[,3]), c(3,4)] <- NA
+    
+    plot(getDate(testsep[,2]), testsep[,3], pch = 20, col = adjustcolor(cols[testsep$Nom_usuel], .4), cex = 1.3, ylim = c(0, 8))
+    
+    # Add legend
+    legend("topleft", col = cols, legend = names(cols), pch = 20, cex = 1)
+    
+    # Highlight specific date
+    abline(v = as.numeric(as.POSIXlt("2024-08-07", format = "%Y-%m-%d")), lwd = 3, col = "red")
+  })
+}
+
+# Run the application 
+shinyApp(ui = ui, server = server)

data/secrets

@@ -0,0 +1,6 @@
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+
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tests/testthat/test-script-helpers.R

@@ -0,0 +1,44 @@
+test_that("sourced getStationData handles request failure without attached httr", {
+  helper_env <- new.env(parent = globalenv())
+  sys.source(testthat::test_path("..", "..", "R", "getStationData.R"), envir = helper_env)
+
+  helper_env$request_api <- function(...) NULL
+
+  expect_null(
+    helper_env$getStationData(
+      start_date = "2024-01-01",
+      end_date = "2024-01-02",
+      station_id = "12345678",
+      headers = list(),
+      timesleep = 0
+    )
+  )
+})
+
+
+test_that("getAllFromCoord returns NULL when every station fetch fails", {
+  helper_env <- new.env(parent = globalenv())
+  sys.source(testthat::test_path("..", "..", "R", "getAllFromCoord.R"), envir = helper_env)
+
+  helper_env$getIdFromCoords <- function(...) {
+    data.frame(
+      Id_station = c("1001", "1002"),
+      Nom_usuel = c("Station A", "Station B"),
+      stringsAsFactors = FALSE
+    )
+  }
+
+  helper_env$getStationData <- function(...) NULL
+
+  expect_null(
+    helper_env$getAllFromCoord(
+      coord = c(44.85, 5.84),
+      start_date = "2024-01-01",
+      end_date = "2024-01-02",
+      allstations = data.frame(),
+      headers = list(),
+      btw_station_sleep = 0,
+      within_statio_sleep = 0
+    )
+  )
+})