Type: Package
Title: An Implementation of Parsing and Writing Configuration File (JSON/INI/YAML/TOML)
Version: 0.3.5
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Depends: R (≥ 3.3.0)
URL: https://github.com/Miachol/configr
BugReports: https://github.com/Miachol/configr/issues
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: jsonlite (≥ 1.2), ini (≥ 0.2), yaml (≥ 2.1.3), RcppTOML (≥ 0.1.3), stringr (≥ 1.2.0), utils, glue
RoxygenNote: 7.1.0
Suggests: testthat, knitr, rmarkdown, prettydoc
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-07-17 09:24:13 UTC; apple
Author: Jianfeng Li ORCID iD [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Repository: CRAN
Date/Publication: 2020-07-17 10:10:02 UTC

Function to access external helps about configurations format or other related information

Description

Function to access external helps about configurations format or other related information

Usage

config.help(name = NULL, show_all_names = FALSE)

Arguments

name

Name or number of helps

show_all_names

Show all urls name

Examples

 config.help()
## Not run: 
 config.help(1)
 config.help('ini_git_search')

## End(Not run)

Merge list file (From config package), list.right will overwrite the element also existed in list.left

Description

Merge list file (From config package), list.right will overwrite the element also existed in list.left

Usage

config.list.merge(list.left = list(), list.right = list())

Arguments

list.left

One list be merged left

list.right

One list be merged right

Value

A list

Examples

config.json <- system.file('extdata', 'config.json', package='configr')
list.left <- list()
list.right <- eval.config(file = config.json)
config.list.merge(list.left, list.right)
list.left <- list(a=c(123,456))
list.right <- list(a=c(4,5,6)) 
config.list.merge(list.left, list.right)

Delete sections in config, just do config[sections] <- NULL

Description

Delete sections in config, just do config[sections] <- NULL

Usage

config.sections.del(config, sections)

Arguments

config

a list of config (eg. generated by read.config)

sections

Sections that need to be deleted

Value

A list of config

Examples

config.json <- system.file('extdata', 'config.json', package = 'configr')
config <- read.config(config.json, file.type = 'json')
config <- config.sections.del(config, 'default')

configr package

Description

Implements the YAML parser, JSON parser, INI parser and TOML parser for R setting and writing of configuration file.

See Also

Useful links:

https://github.com/Miachol/configr

Report bugs at https://github.com/Miachol/configr/issues

Examples


example.toml <- system.file('toml', 'example.toml', package='RcppTOML')
is.toml <- is.toml.file(example.toml)
file.type <- get.config.type(example.toml)
toml.list.raw <- read.config(example.toml)
owner.config <- eval.config(file = example.toml, config = 'owner')
owner.config.name <- eval.config(value = 'name', file = example.toml, config = 'owner')
toml.sections <- eval.config.sections(example.toml)
toml.merged.all <- eval.config.merge(example.toml)
toml.merged.selected <- eval.config.merge(example.toml, sections = c('database', 'owner'))

others <- list(others = list(lastupdate='2017-01-07'))
toml.list.update <- config.list.merge(toml.list.raw, others)

Covert configuration file from JSON/INI/YAML/TOML to JSON/INI/YAML

Description

Covert configuration file from JSON/INI/YAML/TOML to JSON/INI/YAML

Usage

convert.config(
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  out.file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  convert.to = "ini",
  ...
)

Arguments

file

File name of configuration file to read from. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

out.file

Output path of configuration file. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist)

convert.to

JSON/INI/YAML

...

Arguments for read.config and write.config

Value

Logical indicating whether convert success

See Also

fromJSON JSON file will read by this

read.ini INI file will read by this

yaml.load_file YAML file will read by this

Examples

config.json <- system.file('extdata', 'config.json', package='configr')
config <- convert.config(file=config.json, out.file = sprintf('%s/config.ini', tempdir()))

Read from the currently active configuration (JSON/INI/YAML/TOML be supported), 'retreiving either a single named value or all values as a config obj which have 'config', 'configtype', 'file' 'property.

Description

Read from the currently active configuration (JSON/INI/YAML/TOML be supported), 'retreiving either a single named value or all values as a config obj which have 'config', 'configtype', 'file' 'property.

Usage

eval.config(
  value = NULL,
  config = Sys.getenv("R_CONFIG_ACTIVE", "default"),
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  ...
)

Arguments

value

Name of value (NULL to read all values)

config

Name of configuration to read from. Default is the value of 'the R_CONFIG_ACTIVE environment variable (Set to 'default' if the variable does not exist).

file

File name of configuration file to read from. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

...

Arguments for read.config

Value

Either a single value or all values as a list or logical FALSE indicating that is not standard JSON/INI/YAML/TOML format file

See Also

read.config read config by this

eval.config.merge which can merge multiple parameter sets by sections

Examples

config.json <- system.file('extdata', 'config.json', package='configr')
config <- eval.config(file=config.json)
config.extra.parsed.1 <- eval.config(file = config.json, extra.list = list(debug = 'TRUE'))
other.config <- system.file('extdata', 'config.other.yaml', package='configr')
config.extra.parsed.2 <- eval.config(file = config.json, extra.list = list(debug = 'TRUE'), 
other.config = other.config)

Merge config parameter sets by sections.

Description

Merge config parameter sets by sections.

Usage

eval.config.merge(
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  sections = NULL,
  ...
)

Arguments

file

File name of configuration file to read from. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

sections

Need be merged parameter sets, eg. sections=c('default', 'version'), will default to all of config sections

...

Arguments for get.config.type, eval.config.sections, eval.config

Value

A list or logical FALSE indicating that is not standard JSON/INI/YAML/TOML format file

See Also

eval.config.sections which only get all of the mainly parameter sets name in config file, read.config which only read from a config as a list, eval.config which only read one sections as config obj or a value from config file.

Examples

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')
eval.config.merge(config.json)
eval.config.merge(config.ini)
eval.config.merge(config.yaml)
eval.config.merge(config.toml)

Get config file parameter sections

Description

Get config file parameter sections

Usage

eval.config.sections(
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  ...
)

Arguments

file

File name of configuration file to read from. Default is the value of the 'R_CONFIGFILE_ACTIVE' environment variable (Set to 'config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

...

Arguments for read.config

Value

a character vector including the sections infomation of configure file or logical FALSE indicating that is not standard JSON/INI/YAML/TOML format file

See Also

eval.config.merge use this function to get all of sections of config file.

Examples

config.json <- system.file('extdata', 'config.json', package='configr')
eval.config.sections(config.json)

Fetch configuration file and generate a merged list

Description

Fetch configuration file and generate a merged list

Usage

fetch.config(
  links,
  return.files = FALSE,
  destdir = normalizePath("./"),
  keep.basename = TRUE,
  ...
)

Arguments

links

Url or files path that need to be merged, e.g. /tmp/config, http://, ftp://.

return.files

Only save the links configuration files to destdir and not to read and merge the configuration files, default is FALSE

destdir

Fetch configuration files and copy to this directory, default is ./

keep.basename

Whather use the links basename as the saved name or use paste0(tempfile(), '_configr')

...

Extra parameters pass to read.config

Value

A list or a vector

Examples

links <- c(paste0('https://raw.githubusercontent.com/JhuangLab', 
'/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'), 
paste0('https://raw.githubusercontent.com/JhuangLab/BioInstaller', 
'/master/inst/extdata/config/db/db_main.toml'), 
system.file('extdata', 'config.toml', package = 'configr'))
x <- fetch.config(links)

Get config file type retreiving json/ini/yaml or FALSE

Description

Get config file type retreiving json/ini/yaml or FALSE

Usage

get.config.type(file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"), ...)

Arguments

file

File name of configuration file to test. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

...

Arguments for is.json.file, is.ini.file, is.yaml.file, is.toml.file

Value

Character json/ini/yaml/toml or Logical FALSE indicating that is not standard JSON/INI/YAML/TOML format file

See Also

is.json.file, is.ini.file, is.yaml.file, is.toml.file

Examples

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')
get.config.type(file=config.json)
get.config.type(file=config.ini)
get.config.type(file=config.yaml)
get.config.type(file=config.toml)

Test active configuration

Description

Check whether a configuration group is currently active

Usage

is.config.active(config)

Arguments

config

Configuration name

Value

Logical indicating whether the specified configuration is active

Examples

is.config.active('default')

Test active configuration file

Description

Check whether a configuration file is currently active

Usage

is.configfile.active(config.file)

Arguments

config.file

Configuration filename

Value

Logical indicating whether the specified configuration file is active

Examples

is.configfile.active('config.cfg')

Function to check wheather file is INI format

Description

Function to check wheather file is INI format

Usage

is.ini.file(
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  ini.file.debug = FALSE,
  ...
)

Arguments

file

File name of configuration file to test. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

ini.file.debug

If TRUE, it will show error infomation when read INI config, default is FALSE

...

Arguments for read.ini

Value

Logical indicating whether the specified configuration file is INI format

See Also

is.json.file, is.yaml.file, is.toml.file

Examples

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')
print(is.ini.file(config.ini))
print(is.ini.file(config.json))
print(is.ini.file(config.yaml))
print(is.ini.file(config.toml))

Function to check wheather file is JSON format

Description

Function to check wheather file is JSON format

Usage

is.json.file(
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  json.file.debug = FALSE,
  ...
)

Arguments

file

File name of configuration file to test. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

json.file.debug

If TRUE, it will show error infomation when read JSON config, default is FALSE

...

Arguments for readLines and fromJSON

Value

Logical indicating whether the specified configuration file is JSON format

See Also

is.ini.file, is.yaml.file, is.toml.file

Examples

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')
print(is.json.file(config.json))
print(is.json.file(config.ini))
print(is.json.file(config.yaml))
print(is.json.file(config.toml))

Function to check wheather file is TOML format

Description

Function to check wheather file is TOML format

Usage

is.toml.file(
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  toml.file.debug = FALSE,
  ...
)

Arguments

file

File name of configuration file to test. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

toml.file.debug

If TRUE, it will show error infomation when read TOML config, default is FALSE

...

Arguments for parseTOML

Value

Logical indicating whether the specified configuration file is TOML format

See Also

is.json.file is.ini.file, is.yaml.file

Examples

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')
print(is.toml.file(config.json))
print(is.toml.file(config.ini))
print(is.toml.file(config.yaml))
print(is.toml.file(config.toml))

Function to check wheather file is YAML format

Description

Function to check wheather file is YAML format

Usage

is.yaml.file(
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  yaml.file.debug = FALSE,
  ...
)

Arguments

file

File name of configuration file to test. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

yaml.file.debug

If TRUE, it will show error infomation when read YAML config, default is FALSE

...

Arguments for is.json.file, readLines and yaml.load

Value

Logical indicating whether the specified configuration file is YAML format

See Also

is.json.file, is.ini.file, is.toml.file

Examples

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')
print(is.yaml.file(config.yaml))
print(is.yaml.file(config.json))
print(is.yaml.file(config.ini))
print(is.yaml.file(config.toml))

Parse the configuration var format, and replace it by extra.list values

Description

Parse the configuration var format, and replace it by extra.list values

Usage

parse.extra(
  config,
  extra.list = list(),
  other.config = "",
  rcmd.parse = FALSE,
  bash.parse = FALSE,
  glue.parse = FALSE,
  glue.flag = "!!glue",
  global.vars.field = "global_vars"
)

Arguments

config

A list that were generated by read.config/eval.config/eval.config.merge

extra.list

A list that can replace the configuration file 'debug' by list(debug = TRUE), and debug will be setted to TRUE

other.config

Path of another configuration file that can replace the configuration file 'key:value'

rcmd.parse

Logical wheather parse '@>@str_replace('abc', 'b', 'c')@<@' in config to 'acc'

bash.parse

Logical wheather parse '#>#echo $HOME#<#' in config to your HOME PATH

glue.parse

Logical wheather parse '!!glue1:5' in config to ['1','2','3','4','5']; ['nochange', '!!glue(1:5)', 'nochange'] => ['nochange', '1', '2', '3', '4', '5', 'nochange']

glue.flag

A character flag indicating wheater run glue() function to parse (Default is !!glue)

global.vars.field

All vars defined in global.vars.field will as the extra.list params [gloval_var]

Value

A list

Examples

config.json <- system.file('extdata', 'config.json', package='configr')
config.other <- system.file('extdata', 'config.other.yaml', package='configr')
config <- read.config(config.json)
parse.extra(config, list(debug = 'TRUE'))
parse.extra(config, list(debug = 'TRUE'), other.config = config.other)
parse.extra(config, list(debug = 'TRUE'), other.config = config.other, 
rcmd.parse = TRUE)
parse.extra(config, list(debug = 'TRUE'), other.config = config.other, 
rcmd.parse = TRUE, bash.parse = TRUE)

raw <- c('a', '!!glue{1:5}', 'c')
expect.parsed.1 <- c('a', '1', '2', '3', '4', '5', 'c')
list.raw <- list(glue = raw, nochange = 1:10)
parsed <- parse.extra(list.raw, glue.parse = TRUE)

raw <- c('!!glue_numeric{1:5}')
expect.parsed.1 <- c(1, 2, 3, 4, 5)
list.raw <- list(glue = raw, nochange = 1:10)
parsed <- parse.extra(list.raw, glue.parse = TRUE)

Read from the file (JSON/INI/YAML/TOML be supported), retreiving all values as a list.

Description

Read from the file (JSON/INI/YAML/TOML be supported), retreiving all values as a list.

Usage

read.config(
  file = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  extra.list = list(),
  other.config = "",
  rcmd.parse = FALSE,
  bash.parse = FALSE,
  glue.parse = FALSE,
  glue.flag = "!!glue",
  global.vars.field = "global_vars",
  file.type = NULL,
  ...
)

Arguments

file

File name of configuration file to read from. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist and JSON/INI/YAML/TOML format only)

extra.list

A list that can replace the configuration file 'debug' by list(debug = 'TRUE'), and debug will be setted to 'TRUE'

other.config

Path of another configuration file that can replace the configuration file 'key:value'

rcmd.parse

Logical wheather parse '@>@str_replace('abc', 'b', 'c')@<@' that existed in config to 'acc'

bash.parse

Logical wheather parse '#>#echo $HOME#<#' in config to your HOME PATH

glue.parse

Logical wheather parse '!!glue1:5' in config to ['1','2','3','4','5']; ['nochange', '!!glue(1:5)', 'nochange'] => ['nochange', '1', '2', '3', '4', '5', 'nochange']

glue.flag

A character flage indicating wheater run glue() function to parse (Default is !!glue)

global.vars.field

All vars defined in global.vars.field will as the extra.list params [gloval_var]

file.type

Default is no need to specify the variable, file.type will be automatically identify by get.config.type. If the value be specified, the step of filetype identification will be skipped.

...

Arguments for get.config.type, fromJSON, read.ini, yaml.load_file, parseTOML, readLines

Value

All values as a list or logical FALSE indicating that is not standard JSON/INI/YAML/TOML format file

See Also

fromJSON JSON file will read by this

read.ini INI file will read by this

yaml.load_file YAML file will read by this

parseTOML TOML file will read by this

Examples

config.json <- system.file('extdata', 'config.json', package='configr')
config <- read.config(file=config.json)
config.extra.parsed.1 <- read.config(config.json, list(debug = 'TRUE'))
other.config <- system.file('extdata', 'config.other.yaml', package='configr')
config.extra.parsed.2 <- read.config(config.json, list(debug = 'TRUE'), other.config)

Parse configuration string to R list object.

Description

Parse configuration string to R list object.

Usage

str2config(text, ...)

Arguments

text

JSON, YAML, INI or TOML format string.

...

Arguments pass to read.config

Value

List

Examples

json_string <- '{"city" : "Crich"}\n'
yaml_string <- 'foo: 123\n'
json_config <- str2config(json_string)
yaml_config <- str2config(yaml_string)

Write config in a file (JSON/YAML/INI)

Description

Write config in a file (JSON/YAML/INI)

Usage

write.config(
  config.dat,
  file.path = Sys.getenv("R_CONFIGFILE_ACTIVE", "config.cfg"),
  write.type = "ini",
  sections = NULL,
  ...
)

Arguments

config.dat

a list of config (eg. generated by read.config)

file.path

File path of configuration to write. Defaults to the value of the 'R_CONFIGFILE_ACTIVE' environment variable ('config.cfg' if the variable does not exist)

write.type

json/ini/yaml

sections

Sections that need be write in file, default is NULL and use all of sections

...

Arguments for write.ini, prettify, toJSON, as.yaml and cat encoding if not specifield

Value

Logical indicating whether the specified configuration file be writed successful

See Also

toJSON convert a list to JSON string, prettify convert a JSON string to user friendly view, write.ini write a list in a INI format file, as.yaml convert a list to YAML format

Examples

list.test <- list(a=c(123,456))
out.yaml <- sprintf('%s/test.yaml', tempdir()) 
write.config(list.test, out.yaml, write.type = 'yaml')