resolve conflicts master

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: antaresRead
 Type: Package
 Title: Import, Manipulate and Explore the Results of an 'Antares' Simulation
-Version: 2.5.2
+Version: 2.6.1
 Authors@R: c(
     person("Tatiana", "Vargas", email = "[email protected]", role = c("aut", "cre")),
     person("Jalal-Edine", "ZAWAM", role = "aut"),
@@ -48,6 +48,7 @@ Suggests:
     parallel,
     htmltools
 RoxygenNote: 7.2.2
+Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Encoding: UTF-8
 biocViews: Infrastructure, DataImport

NAMESPACE

@@ -51,6 +51,7 @@ export(readAntaresClusters)
 export(readBindingConstraints)
 export(readClusterDesc)
 export(readClusterResDesc)
+export(readClusterSTDesc)
 export(readDigestFile)
 export(readIni)
 export(readIniAPI)

NEWS.md

@@ -1,18 +1,49 @@
 > Copyright © 2016 RTE Réseau de transport d’électricité
 
-
-# antaresRead 2.5.3
+# antaresRead 2.7.0
 
 ### Breaking changes (Antares v8.7) : 
 
 * Existing function `readBindingConstraints()` (cf. Antares v8.7 changelog)
 
-# antaresRead 2.5.2
 
-BREAKING CHANGES:
+# antaresRead 2.6.1 (devlopment)
+
+BUGFIXES :  
+
+* `setSimulationPathAPI()` :  
+  - returns an API exception if the requested study ID is incorrect 
+  - `simulation` the simulation parameter works with negative values within the limit of the number of simulations
+* correction in `readClusterDesc()` calls to add "opts"
+
+
+# antaresRead 2.6.0
+
+NEW FEATURES (Antares v8.6, cf. Antares v8.6 changelog) :
+
+* `readClusterSTDesc()` read "short-term storage" clusters parameters (input files of an antares study)
+
+
+BREAKING CHANGES (Antares v8.6) :
+
+* `readInputTS()` is now compatible to read time series with :  
+  - "short-term storage"  
+  - "mingen" (pmin hydro value)
+* `setSimulationPath()` has new parameter `areasWithSTClusters` (name of area with "st-storage" cluster)
+
+
+BUGFIXES : 
 
 * `setSimulationPathAPI` generate new global parameter `sleep` to add timer to API request
+* Correction of `.importOutput()` to use `readAntares()` with `parallel == TRUE` in shiny application
+* `setSimulationPathAPI()` delete a redundant API request
+* `readClusterDesc()` minor fix in API mode + fix if no cluster exists => return specific error message
+* `readIniAPI()` read well file `generaldata` for sections "playlist" and "variables selection"
+
+
+DATA : 
 
+* A test study in tar.gz format is available in version `v8.6.0`
 
 
 # antaresRead 2.5.1

R/API-methods.R

@@ -55,7 +55,16 @@ api_get <- function(opts, endpoint, ..., default_endpoint = "v1/studies") {
   #fix for skipping 404 when some output is missing
   url_elements <- strsplit(result$url, "%2F")[[1]]
   condition_status_check <- !(!is.na(url_elements[4]) & url_elements[4] %in% c("economy","adequacy") & result$status_code == 404)
-  if (condition_status_check) stop_for_status(result) else warn_for_status(result)
+  if(condition_status_check){
+    mess_error <- content(result)
+    if(!is.null(names(mess_error)))
+      mess_error <- paste0("\n[Description] : ", mess_error$description,
+                           "\n[Exception] : ", mess_error$exception)
+    else
+      mess_error <- NULL
+    stop_for_status(result, task = mess_error)
+    }else 
+      warn_for_status(result)
   content(result)
 }
 
@@ -90,7 +99,13 @@ api_post <- function(opts, endpoint, ..., default_endpoint = "v1/studies") {
     config = config,
     ...
   )
-  stop_for_status(result)
+  api_content <- content(result)
+  if(!is.null(names(api_content)))
+    api_content <- paste0("\n[Description] : ", api_content$description,
+                         "\n[Exception] : ", api_content$exception)
+  else
+    api_content <- NULL
+  stop_for_status(result, task = api_content)
   content(result)
 }
 

R/giveSize.R

@@ -171,7 +171,7 @@ setRam <- function(x){
   clusWithData <- data.table()
   if(!is.null(clusters))
   {
-    clusWithData  <- tryCatch(readClusterDesc(), error = function(e) data.table())
+    clusWithData  <- tryCatch(readClusterDesc(opts = opts), error = function(e) data.table())
     if("all" %in% clusters){
       enabled <- TRUE
       if("enabled" %in% names(clusWithData))

R/importInput.R

@@ -157,6 +157,12 @@
                  inputTimeStep = "hourly", type = "matrix")
 }
 
+# "mingen" (v860)
+.importmingen <- function(area, timeStep, opts, ...){
+  .importInputTS(area, timeStep, opts, "hydro/series/%s/mingen.txt", "mingen", 
+                 inputTimeStep = "hourly", type = "matrix")
+}
+
 .importHydroStorageInput <- function(area, timeStep, opts, ...) {
   inputTimeStepV <- ifelse(opts$antaresVersion >= 650, yes = "daily", no = "monthly")
   .importInputTS(area, timeStep, opts, "hydro/series/%s/mod.txt", "hydroStorage", 
@@ -421,3 +427,94 @@
 #   out <- gsub(" ", "%20", out)
 # }
 
+
+# "st-storage" (v860)
+.importSTStorage <- function(area, timeStep, opts, ...){
+
+  if (!area %in% opts$areasWithSTClusters) 
+    return(NULL)
+
+  if(!"api" %in% opts$typeLoad){
+    clusters <- list.files(
+      file.path(opts$inputPath, 
+                "st-storage/series", 
+                area)
+      )
+
+    # "st-storage" have 5 txt files output for each cluster
+    list_names_txt_files <- unique(
+      list.files(
+        file.path(opts$inputPath,  
+                  "st-storage/series", 
+                  area, 
+                  clusters)
+        )
+    )
+
+    list_names_less_txt <- sub(pattern = ".txt", 
+                               replacement = "", 
+                               x = list_names_txt_files)
+
+  } else {
+    list_info_clusters <- read_secure_json(
+      file.path(opts$inputPath, 
+                "st-storage/series", 
+                area), 
+      token = opts$token, 
+      timeout = opts$timeout, 
+      config = opts$httr_config
+      )
+
+    clusters <- names(list_info_clusters)
+
+    files_names <- names(list_info_clusters[[1]])
+
+    list_names_txt_files <- paste0(files_names, ".txt")
+    list_names_less_txt <- files_names 
+  }
+
+  # read TS for every cluster
+  ldply(clusters, function(cl) {
+    pattern <- paste0("%s/%s/%%s/", 
+                      list_names_txt_files)
+    filePatterns <- sprintf(pattern, 
+                            "st-storage/series", area)
+
+    res <- lapply(filePatterns, 
+                  function(.x){
+                    index_name_file <- which(filePatterns %in% .x)
+
+                    res_temp <- .importInputTS(area= cl, 
+                                               timeStep= timeStep, 
+                                               opts= opts, 
+                                               fileNamePattern= .x,
+                                               colnames= "st-storage",
+                                               inputTimeStep = "hourly", 
+                                               type = "matrix")
+                    res_temp$name_file <- list_names_less_txt[index_name_file]
+                    res_temp
+                    })
+
+    res <- rbindlist(res)
+
+    if (is.null(res)) 
+      return(NULL)
+
+    res$area <- area
+    res$cluster <- cl
+
+    setcolorder(res, 
+                c("area", 
+                  "cluster", 
+                  "timeId", 
+                  setdiff(
+                    names(res), 
+                    c("area", 
+                      "cluster", 
+                      "timeId")))
+                )
+  })
+
+  # added a column "name_file" to tag the file name
+
+}

R/importOutput.R

@@ -139,7 +139,7 @@
       res <- llply(
         1:nrow(args), 
         function(i) {
-          incProgress(1/n, detail = paste0("Importing ", folder, " data"))
+          if(showProgress){ incProgress(1/n, detail = paste0("Importing ", folder, " data")) }
           data <- NULL
           try({
             if (!sameNames) {

R/readAntaresClusters.R

@@ -18,7 +18,7 @@ readAntaresClusters <- function(clusters, selected = c("production", "NP Cost",
     stop("Cannot use 'readAntaresClusters' in 'Input' mode.")
 
   ##Add check control for all
-  allClusters <- readClusterDesc()[, c("area","cluster")]
+  allClusters <- readClusterDesc(opts = opts)[, c("area","cluster")]
   ind_cluster <- which(tolower(allClusters$cluster) %in% .checkArg(tolower(clusters), 
                                                                    tolower(unique(allClusters$cluster)), 
                                                                    "clusters %s do not exist in the simulation."))

R/readClusterDesc.R

@@ -32,6 +32,8 @@
 #' \code{readClusterDesc} : read thermal clusters
 #' 
 #' \code{readClusterResDesc} : read renewable clusters (Antares >= V8.1)
+#' 
+#' \code{readClusterSTDesc} : read st-storage clusters (Antares >= V8.6)
 #'
 #' @examples
 #' 
@@ -43,6 +45,9 @@
 #' # renewable
 #' readClusterResDesc()
 #' 
+#' # st-storage
+#' readClusterSTDesc()
+#' 
 #' # By default, the function reads cluster descriptions for the default study,
 #' # but it is possible to specify another study with parameter "opts"
 #' sim1 <- setSimulationPath()
@@ -69,10 +74,22 @@ readClusterResDesc <- function(opts = simOptions()) {
      is.null(opts$parameters$`other preferences`$`renewable-generation-modelling`)){
     stop("readClusterDesc is available only on studies with 'renewable-generation-modelling' = 'clusters' (and Antares >= 8.1)", call. = FALSE)
   }
-  .readClusterDesc(opts = simOptions(), dir = "renewables/clusters")
+  .readClusterDesc(opts = opts, dir = "renewables/clusters")
 }
 
 
+#' @export
+#'
+#' @rdname readClusterDesc
+readClusterSTDesc <- function(opts = simOptions()) {
+  if (opts$antaresVersion < 860) {
+    stop("readClusterSTDesc is available only on Antares >= 8.6)", call. = FALSE)
+  }
+  .readClusterDesc(opts = opts, dir = "st-storage/clusters")
+}
+
+
+
 .readClusterDesc <- function(opts = simOptions(), 
                              dir = "thermal/clusters") {
 
@@ -104,7 +121,10 @@ readClusterResDesc <- function(opts = simOptions()) {
       if(nrow(clusters)==0)return(NULL)
       clusters$area <- Y1
       clusters[, .SD, .SDcols = order(names(clusters))]
-    },jsoncld, names(jsoncld)), fill = TRUE)
+    },jsoncld, names(jsoncld), SIMPLIFY = FALSE), fill = TRUE)
+
+    if(length(res) == 0) 
+      stop("Cannot find cluster description.", call. = FALSE)
 
     res <-  res[, .SD, .SDcols = c("area", "name", "group", names(res)[!names(res) %in%c("area", "name", "group")])]
 

R/readIniFile.R

@@ -97,12 +97,58 @@ readIniFile <- function(file, stringsAsFactors = FALSE) {
 #' @export
 #' @rdname read-ini
 readIniAPI <- function(study_id, path, host, token = NULL) {
-  api_get(
+  api_get_ini_file <- api_get(
     opts = list(host = host, token = token),
     endpoint = paste0(study_id, "/raw"),
     query = list(
       path = path,
       formatted = TRUE
     )
   )
+  # reformat list contains unnamed list
+  .format_list(api_get_ini_file)
+}
+
+# reformat list from JSON format 
+.format_list <- function(list_x){
+  # check list to find sub list
+  check_class_list <- lapply(list_x, function(x) 
+    lapply(x, class) %in% "list")
+
+  is_true_list <- lapply(check_class_list, function(x) 
+    any(x %in% TRUE))
+
+  index_true <- which(is_true_list %in% TRUE)
+
+  # reformat sub list
+  list_to_reformat <- list_x[index_true]
+
+  list_to_reformat <- lapply(list_to_reformat, function(x){
+    index_list <- which(
+      lapply(x, class) %in% "list")
+
+    # reformat only unnamed list
+    if(is.name(x[index_list]))
+      return(x)
+    else{
+      elements <- unlist(x[index_list], use.names = FALSE)
+      if(class(elements)%in%"character"){
+        elements <- paste("'", elements, "'", sep="", collapse=",")
+        elements <- paste0("[", elements, "]")
+      }else{
+        elements <- paste0(elements, collapse= ",")
+        elements <- paste0("[", elements, "]")
+      }
+      x[index_list] <- elements
+      x
+    }
+  })
+
+  # return original list 
+  if(identical(index_true, integer(0)))
+    list_x
+  else
+    # return list reformated
+    append(list_x[-index_true], 
+           list_to_reformat)
 }

R/readInputClusters.R

@@ -41,7 +41,7 @@ readInputThermal <- function(clusters = NULL, thermalModulation = FALSE, thermal
     if (!foreach::getDoParRegistered()) stop("Parallelized importation impossible. Please register a parallel backend, for instance with function 'registerDoParallel'")
   }
 
-  allAreasClusters <- readClusterDesc()[area %in% opts$areasWithClusters, c("area", "cluster")]
+  allAreasClusters <- readClusterDesc(opts = opts)[area %in% opts$areasWithClusters, c("area", "cluster")]
   allClusters <- unique(allAreasClusters$cluster)
   # Manage special value "all"
   if(identical(clusters, "all")) clusters <- allClusters
@@ -139,7 +139,7 @@ readInputRES <- function(clusters = NULL, opts = simOptions(),
     if (!foreach::getDoParRegistered()) stop("Parallelized importation impossible. Please register a parallel backend, for instance with function 'registerDoParallel'")
   }
 
-  allAreasClusters <- readClusterResDesc()[area %in% opts$areasWithResClusters, c("area", "cluster")]
+  allAreasClusters <- readClusterResDesc(opts = opts)[area %in% opts$areasWithResClusters, c("area", "cluster")]
   allClusters <- unique(allAreasClusters$cluster)
   # Manage special value "all"
   if(identical(clusters, "all")) clusters <- allClusters