# Install this package directly from CRAN by running (from within R):
install.packages('configr')

# Install the cutting edge development version from GitHub:
# install.packages("devtools")
devtools::install_github("Miachol/configr")

library(configr)

# Demo files
config.json <- system.file('extdata', 'config.json', package='configr')
config.ini <- system.file('extdata', 'config.ini', package='configr')
config.yaml <- system.file('extdata', 'config.yaml', package='configr')
config.toml <- system.file('extdata', 'config.toml', package='configr')
config.glob <- system.file('extdata', 'config.global.toml', package='configr')

# Check the type of configuration file
is.json <- is.json.file(file = config.json)
is.ini <- is.ini.file(file = config.ini)
is.yaml <- is.yaml.file(file = config.yaml)
is.toml <- is.toml.file(file = config.toml)

# Check the type of configuration file (Debug mode)
is.json <- is.json.file(file = config.yaml, json.file.debug = T)
is.ini <- is.ini.file(file = config.json, ini.file.debug = T)
is.yaml <- is.yaml.file(file = config.toml, yaml.file.debug = T)
is.toml <- is.toml.file(file = config.yaml, toml.file.debug = T)

# Query the type of configuration file
json <- get.config.type(file = config.json) 
ini <- get.config.type(file = config.ini) 
yaml <- get.config.type(file = config.yaml) 
toml <- get.config.type(file = config.toml) 

# Read the whole configuration file
json.list <- read.config(file = config.json)
ini.list <- read.config(file = config.ini)
yaml.list <- read.config(file = config.yaml)
toml.list <- read.config(file = config.toml) 

# Read specific section of configuration file (default is 'default' section)
# Configuration type, section, and path were added to the parsed object
config.json.obj <- eval.config(file = config.json)
config.ini.obj <- eval.config(file = config.ini)
config.yaml.obj <- eval.config(file = config.yaml)
config.toml.obj <- eval.config(file = config.toml)

# Query all section names
json.sections <- eval.config.sections(file = config.json)
ini.sections <- eval.config.sections(file = config.ini)
yaml.sections <- eval.config.sections(file = config.yaml)
toml.sections <- eval.config.sections(file = config.toml)

# Merge multiple sections, default is all
# Reduce a layer of configuration file
json.config.all <- eval.config.merge(file = config.json)
ini.config.all <- eval.config.merge(file = config.ini)
yaml.config.all <- eval.config.merge(file = config.yaml)
toml.config.all <- eval.config.merge(file = config.toml)

# Parse string to configuration list object
json_string <- '{"city" : "Z\\u00FCrich"}\n'
yaml_string <- 'foo: 123\n'
json_config <- str2config(json_string)
yaml_config <- str2config(yaml_string)

# Download and parse files from remote websits
links <- c('https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml', 
           'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_main.toml')
fetch.config(links)

# Convert YAML format to JSON format
convert.config(file = config.yaml, out.file = tempfile(, fileext = ".json"), 
  convert.to = "JSON")

# Write JSON format file
list.test <- list(a=c(123,456))
out.fn <- sprintf("%s/test.json", tempdir())

write.config(config.dat = list.test, file.path = out.fn, 
  write.type = "json")

# Write JSON format file with 2 indent
write.config(config.dat = list.test, file.path = out.fn, 
  write.type = "json", indent = 2)

# Write YAML format file
out.fn <- sprintf("%s/test.yaml", tempdir())
write.config(config.dat = list.test, file.path = out.fn, 
  write.type = "yaml")
# Write YAML format file with 4 indent
write.config(config.dat = list.test, file.path = out.fn, 
  write.type = "yaml", indent = 4)

# Write TOML format file
# !! You need install python and toml package
# pip install toml
out.fn <- sprintf("%s/test.toml", tempdir())
write.config(config.dat = list.test, file.path = out.fn, 
  write.type = "toml")

out.fn <- sprintf("%s/test.ini", tempdir())

# Write INI format file
write.config(config.dat = list.test, file.path = out.fn, 
  write.type = "ini")

# Write INI format file. It only includes given sections.
write.config(config.dat = list.test, file.path = out.fn, sections = "a",
  write.type = "ini")

# Demo of extended parse functions
# 
# Read raw file by jsonlite, yaml, INI and RcppTOML packages
config.1 <- read.config(file = config.json)
other.config <- system.file('extdata', 'config.other.yaml', package='configr')

# Replace any string "{{debug}}" and "{{debug2}}" to "self" and "self2" respectively
config.2 <- read.config(file = config.json, 
  extra.list = list(debug = "self", debug2 = "self2"))

# Replace any string "{{debug}}" and "{{debug2}}" to "self" and "self2" respectively
# Then replace {{key:yes_flag}} to the value of other.config key's yes_flag and no_flag
config.3 <- read.config(file = config.json, 
  extra.list = list(debug = "self", debug2 = "self2"), 
  other.config = other.config)

# Replace any string "{{debug}}" and "{{debug2}}" to "self" and "self2" respectively
# Then replace {{key:yes_flag}} to value in other.config key's yes_flag and no_flag
# Then replace @>@ Sys.Date() @<@ to R command result ...
config.4 <- read.config(file = config.json, 
  extra.list = list(debug = "self", debug2 = "self2"), 
  other.config = other.config, rcmd.parse = T)

config.5 <- parse.extra(config.1, 
  extra.list = list(debug = "self", debug2 = "self2"), 
  other.config = other.config, rcmd.parse = T)
  
# Replace any items contained string "{{debug}}" to "self" and "debug2" to "self2"
# Then replace {{key:yes_flag}} to value in other.config key's yes_flag and no_flag
# Then replace @>@ Sys.Date() @<@ to R command executed result ...
# Then replace #>#echo bash#<# to system() executed result
config.6 <- parse.extra(config.1, 
  extra.list = list(debug = "self", debug2 = "self2", yes = "1", no = "0"), 
  other.config = other.config, rcmd.parse = T, bash.parse = T)

# Use glue() to parse "{value or R CMD}"
# It will changes the length of a vector if returned value is a vector
raw <- c("a", "!!glue{1:5}", "c")
list.raw <- list(glue = raw, nochange = 1:10)
parsed <- parse.extra(list.raw, glue.parse = TRUE, glue.flag = "!!glue")
expect.parsed.1 <- c("a", "1", "2", "3", "4", "5", "c")
expect.parsed.2 <- list(glue = expect.parsed.1, nochange = 1:10)


# Global vars parse (new feature in v0.3.4)
# 
config_no_parsed_global <- read.config(config.glob, global.vars.field = NULL)
config_parsed <- read.config(config.glob)

# Delete a section in a configuration object
config.partial <- config.sections.del(config.1, "default")

# Show all help urls stored in configr
config.help()
# Open the url in browser
config.help('toml_stackoverflow_search')
# Or use the row number to access
config.help(23)