add bash Rscript

inst/script/friendlyr.R

+#!/usr/lib/R/bin/Rscript
+
+# Jean-Marie Lepioufle
+# NILU - nilu.no
+# 2019-02-21
+# Get timeseries from a service by using friendlyr
+
+'friendlyr
+
+Usage:
+  friendlyr.R -service <service> -fromDate <fromDate> -toDate <toDate> -precision <precision> -timeResolution <timeResolution> -element_id <element_id> -station_id <station_id> -username <username> -password <password> -result <result> -name <name>
+  conv.R (-h | --help)
+  conv.R --version
+
+Options:
+  -h --help         Show this screen.
+  --version         Show version.
+
+Outcomes:
+  timeserie:  Timeserie of as a friendlyts data.frame.
+
+' -> doc
+
+
+#library(docopt)
+arguments <- docopt::docopt(doc, version = 'conv version 0.0.1')
+
+###################
+# requirement     #
+###################
+suppressPackageStartupMessages(require("friendlyr"))
+
+###################
+# init parameters #
+###################
+
+cat("Initialising parameters... \n")
+
+
+service <- tryCatch({
+
+  res <- as.character(arguments$service)
+  if(!(res %in% c("luftlyr","innoly","frostlyr","d.luft.oslyr","d.eipalyr","d.eimetlyr"))) stop("'service' need to be one of these: 'luftlyr','innoly','frostlyr','d.luft.oslyr','d.eipalyr','d.eimetlyr'")
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'service':  ",err))
+  print("It will crash.")
+
+})
+
+fromDate <- tryCatch({
+
+  res <- as.character(arguments$fromDate)
+  # add some filter
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'fromDate':  ",err))
+  print("It will crash.")
+
+})
+
+
+toDate <- tryCatch({
+
+  res <- as.character(arguments$toDate)
+  # add some filter
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'toDate':  ",err))
+  print("It will crash.")
+
+})
+
+precision <- tryCatch({
+
+  res <- as.character(arguments$precision)
+  if(!(res %in% c("second","minute","hourly","daily","monthly","yearly"))) stop("'service' need to be one of these: 'second','minute','hourly','daily','monthly','yearly'")
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'precision':  ",err))
+  print("It will crash.")
+
+})
+
+timeResolution <- tryCatch({
+
+  res <- as.character(arguments$timeResolution)
+  if(!(res %in% c("second","minute","hourly","daily","monthly","yearly"))) stop("'service' need to be one of these: 'second','minute','hourly','daily','monthly','yearly'")
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'timeResolution':  ",err))
+  print("It will crash.")
+
+})
+
+element_id <- tryCatch({
+
+  res <- as.character(arguments$element_id)
+  # add some filter
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'element_id':  ",err))
+  print("It will crash.")
+
+})
+
+station_id <- tryCatch({
+
+  res <- as.character(arguments$station_id)
+  # add some filter
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'station_id':  ",err))
+  print("It will crash.")
+
+})
+
+username <- tryCatch({
+
+  res <- as.character(arguments$username)
+  # add some filter
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'username':  ",err))
+  print("It will crash.")
+
+})
+
+password <- tryCatch({
+
+  res <- as.character(arguments$password)
+  # add some filter
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'password':  ",err))
+  print("It will crash.")
+
+})
+
+# get path of where to store the result
+result <- tryCatch({
+
+  res <- normalizePath(file.path(as.character(arguments$result),"friendlyr"),mustWork = FALSE)
+  dir.create(res, showWarnings = FALSE, recursive = TRUE)
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'result':  ",err))
+  print("'result' get its default value: '~'")
+
+  res <- normalizePath(file.path(path.expand('~'),"friendlyr"),mustWork = FALSE)
+  dir.create(res, showWarnings = FALSE, recursive = TRUE)
+  return(res)
+
+})
+
+
+name <- tryCatch({
+
+  res <- as.character(arguments$name)
+  # add some filter
+  res
+
+}, error = function(err) {
+
+  print(paste("Error in argument 'name':  ",err))
+  print("It will crash.")
+
+})
+
+
+#######################
+# get timeseries data #
+#######################
+df <- friendlyr::ts(service=service,username=username,password=password,
+                 fromDate=fromDate,toDate=toDate,precision=precision,timeResolution=timeResolution,
+                 element_id=element_id,station_id=station_id)
+
+
+#save
+pathfile <- normalizePath(file.path(path, paste0(name,".csv")),mustWork = FALSE)
+write.csv(df,file=pathfile,row.names=FALSE)

inst/script/readme.md

+## Friendlyr in bash
+
+Author: Jean-Marie Lepioufle, [NILU](https://nilu.no).
+
+Date: 2019-02-21.
+
+**Purpose** :
+
+- Gathering long timeseries from different internal and external services.
+
+**Available services** :
+
+- luftkval (NILU): "luftlyr"
+- innosense (NILU): "innolyr"
+- frost (MET): "frostlyr"
+- embedded dataset luftkval.oslo10: "d.luft.oslyr"
+- embedded dataset EPA Ireland: "d.eipalyr"
+- embedded dataset MetOffice Ireland: "d.eimetlyr"
+
+**Component** :
+
+- friendlyr.sh: run friendlyr.R with possibility of asynchronous loop.
+- friendlyr.R: Gather data
+
+**Remarks** :
+
+Friendlyr required installation of libraries from NILU's gitlab.
+
+A full frontend version of friendlyr is available through [rØya](https://git.nilu.no/oya/roya) service
+
+### Pre-requisities
+
+#### Get easily command-line interface through Rscript.
+
+In order to get a command-line interface through Rscript, you need to install docopt packages in R.
+
+```R
+install.packages("docopt")
+```
+#### Get the right packages to run the case study
+
+The package batqa and its dependencies enable to optimize a model.
+For our case study, and as suggested in batqa DESCRIPTION, need one to install other packages: metrics, friendlyr, d.luft.oslyr, friendlyts and ranger.
+
+```R
+# devtools Version: 2.0.1.9000
+# devtools::install_github("r-lib/devtools")
+library("devtools")
+devtools::install_git("https://git.nilu.no/rfriendlyr/friendlyr.git")
+```
+
+#### R script as executables
+The path to Rscript listed in the shebang line of the file friendlyr.R needs to be in your PATH variable.
+
+Check the path of your Rscript.
+```shell
+which Rscript
+```
+Then paste it into your .bashrc
+```shell
+echo 'export PATH="$PATH:/usr/lib/R/bin/Rscript"' >> ~/.bashrc
+```
+
+The script friendlyr.R needs then to be executable.
+
+```shell
+cd </path/to/friendlyr.R>
+
+chmod +x friendlyr.R
+```
+Then the script friendlyr.R is executable by writing:
+
+```shell
+./friendlyr.R -service <service> -fromDate <fromDate> -toDate <toDate> -precision <precision> -timeResolution <timeResolution> -element_id <element_id> -station_id <station_id> -username <username> -password <password> -result <result> -name <name>
+```
+
+
+#### shell script as executable
+In order to gather long timeseries of data, the request is splitted. The script friendly.sh focuses on this.
+
+The script friendlyr.sh needs to be executable.
+
+```shell
+cd </path/to/friendlyr.sh>
+
+chmod +x friendlyr.sh
+```
+Then the script friendlyr.sh is executable by writing:
+
+```shell
+ . ./friendlyr.sh <service> <fromDate> <toDate> <precision> <timeResolution> <element_id> <station_id> <username> <password> <result>
+```
+
+
+
+### Usage
+
+Parameters <station> and <batea_type> are always arrays.
+
+```shell
+
+# example 1
+cd </path/to/bat_oslo.R>
+
+./friendlyr.R -service "frostlyr" -fromDate "2016/11/6 00:00:00" -toDate "2016/11/10 00:00:00" -precision "hourly" -timeResolution "hourly" -element_id "air_temperature" -station_id "SN18700" -username "****" -password "*****" -result "~/" -name "1"
+
+# example 2
+
+cd </path/to/bat_oslo.sh>
+
+element_id=("7")
+b_type=("r")
+./friendlyr.R -service "frostlyr" -fromDate "2016/11/6 00:00:00" -toDate "2016/11/10 00:00:00" -precision "hourly" -timeResolution "hourly" -element_id "air_temperature" -station_id "SN18700" -username "****" -password "*****" -result "~/" -name "1"
+
+# example 2
+station=("7" "11" "9")
+b_type=("r")
+. ./bat_oslo.sh "1" station b_type "mh_pw" 10 "~/"
+
+# example 3
+station=("7" "11" "9")
+b_type=("r" "or" "sor")
+. ./bat_oslo.sh "1" station b_type "mh_pw" 10 "~/"
+
+```
+
+
+```R
+
+
+
+# dates
+timeResolution <- "hourly"
+precision <- "hourly"
+fromDate <- "2013010100"
+toDate <- "2018060100"
+tmp <- timemanip::timeserie(timeResolution="monthly",fromPeriod=fromDate,toPeriod=toDate,precision=precision)
+
+from <- tmp$seqPeriod[1:(tmp$nbStep-1)]
+
+to <- tmp$seqPeriod[2:(tmp$nbStep)]
+if (length(to)>1) {
+  to[1:(length(to)-1)] <- timemanip::addition_nonsec(to[1:(length(to)-1)],timeResolution=timeResolution,v=-1)
+}
+
+
+# elements
+element_id <- c("sum(precipitation_amount PT1H)",
+             "wind_from_direction",
+             "wind_speed",
+             "surface_air_pressure",
+             "mean(surface_downwelling_shortwave_flux_in_air PT1H)",
+             "air_temperature",
+             "relative_humidity")
+
+
+# stations
+location <- "Oslo, Norway"
+frost_meta <- friendlyr::meta(service="frostlyr",element_id=element_id,location=location,username=username,password=password)
+station_id <- as.character(frost_meta$ID)
+
+
+```