.exe umbenannt

NAMESPACE

@@ -5,6 +5,7 @@ export("%>%")
 export(create_term_match_table)
 export(files_in_group)
 export(flatten_json)
+export(generate_json)
 export(gradient_tables)
 export(group_count)
 export(instrument_names)
@@ -13,6 +14,5 @@ export(one_gradient_table)
 export(one_group_match_terms)
 export(save_all_groups)
 export(save_group_table)
-export(use_rawMetaAsJson)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")

R/additional_functions.R

@@ -1,14 +1,14 @@
 #' Number of groups in the json file
 #'
-#' @param json A JSON file generated by the function "use_rawMetaAsJson()" or by using rawMetaAsJson.exe externaly.
+#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
 #'
 #' @return Count of groups in the JSON file.
 #'
 #' @examples
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' group_count(json)
 #'
@@ -24,7 +24,7 @@ group_count <- function(json)
 
 #' Filenames of one group
 #'
-#' @param json A JSON file generated by the function "use_rawMetaAsJson()" or by using rawMetaAsJson.exe externaly.
+#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
 #' @param group_number An index that determines the group.
 #'
 #' @return A list of filenames belonging to the choosen group.
@@ -33,7 +33,7 @@ group_count <- function(json)
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' files_in_group(json, 1)
 #'
@@ -51,7 +51,7 @@ files_in_group <- function(json, group_number)
 
 #' Get instrument names
 #'
-#' @param json A JSON file generated by the function "use_rawMetaAsJson()" or by using rawMetaAsJson.exe externaly.
+#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
 #' @param group_number An index that determines the group.
 #'
 #' @return A list of instruments used in the choosen group.
@@ -60,7 +60,7 @@ files_in_group <- function(json, group_number)
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' instrument_names(json, 1)
 #'

R/data.R

@@ -11,3 +11,10 @@
 #'   ...
 #' }
 "tmt_list"
+
+
+#' Already generated JSON example file.
+#'
+#' @format A JSON file, read by jsonlite::fromJSON()
+#'
+"testfile_json"

R/gradient_functions.R

@@ -52,7 +52,7 @@ gradient_as_string <- function(flat_json, group_number)
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' flat_json <- flatten_json(json)
 #'
@@ -94,7 +94,7 @@ one_gradient_table <- function(flat_json, group_number, lc_pump = "Thermo EASY-n
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' flat_json <- flatten_json(json)
 #'

R/load_meta_functions.R

@@ -8,18 +8,18 @@
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' @export
 
-use_rawMetaAsJson <- function(path_data)
+generate_json <- function(path_data)
 {
   new_file <- tempfile()
-  path_rawMetaAsJson <- system.file(
-    file.path('bin','rawMetaAsJson.exe'),
+  path_MARMoSET_exe <- system.file(
+    file.path('bin','MARMoSET.exe'),
     package = 'MARMoSET', mustWork = TRUE)
 
-  assertive.files::assert_all_are_executable_files(path_rawMetaAsJson, warn_about_windows = F)
+  assertive.files::assert_all_are_executable_files(path_MARMoSET_exe, warn_about_windows = F)
 
   path_data_is_ok <- function(x){ assertive.files::is_dir(x) || assertive.files::is_readable_file(x, warn_about_windows = F)}
   assertive.base::assert_engine( path_data_is_ok, path_data,
@@ -32,7 +32,7 @@ use_rawMetaAsJson <- function(path_data)
     stop("Function is only working under windows.")
   }
 
-  system(command = paste(path_rawMetaAsJson, paste0('"',path_data, '"'), new_file),
+  system(command = paste(path_MARMoSET_exe, paste0('"',path_data, '"'), new_file),
          intern  = T)
 
   json <- jsonlite::fromJSON(new_file)
@@ -43,15 +43,15 @@ use_rawMetaAsJson <- function(path_data)
 
 #' flattening JSON
 #'
-#' @param json A JSON file generated by the function "use_rawMetaAsJson()" or by using rawMetaAsJson.exe externaly.
+#' @param json A JSON file generated by the function "generate_json()" or by using MARMoSET.exe externaly.
 #'
 #' @return A flattened Json for better access.
 #'
 #' @examples
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' flat_json <- flatten_json(json)
 #'

R/output_functions.R

@@ -8,7 +8,7 @@
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' flat_json <- flatten_json(json)
 #'
@@ -31,14 +31,29 @@ save_group_table <- function(groups_vector, output_path, group_number)
   assertive.files::assert_all_are_dirs(output_path %>% pathological::decompose_path() %>% .$dirname)
   assertive.strings::assert_all_are_non_empty_character(output_path %>% pathological::decompose_path() %>% .$filename)
 
-  if (output_path %>% pathological::decompose_path() %>% .$extension != "txt")
+  if (output_path %>% pathological::decompose_path() %>% .$extension %>% stringi::stri_endswith(fixed = "txt"))
   {
-    output_path %<>% pathological::decompose_path() %>%
+    output_path_txt <- output_path
+  }else
+  {
+    output_path_txt <- pathological::decompose_path(output_path) %>%
       magrittr::inset2('extension', value = paste(.$extension,'txt', sep = '')) %>%
       pathological::recompose_path()
   }
 
-  utils::write.table(groups_vector[[group_number]], file = output_path, sep = "\t")
+  utils::write.table(groups_vector[[group_number]], file = output_path_txt, sep = "\t")
+
+  if (output_path %>% pathological::decompose_path() %>% .$extension %>% stringi::stri_endswith(fixed = "csv"))
+  {
+    output_path_csv <- output_path
+  }else
+  {
+    output_path_csv <- pathological::decompose_path(output_path) %>%
+      magrittr::inset2('extension', value = paste(.$extension,'csv', sep = '')) %>%
+      pathological::recompose_path()
+  }
+
+  utils::write.csv(groups_vector[[group_number]], file = output_path_csv)
 }
 
 utils::globalVariables('.')
@@ -53,7 +68,7 @@ utils::globalVariables('.')
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' flat_json <- flatten_json(json)
 #'

R/reexports.R

@@ -1,14 +1,14 @@
 #' magrittr forward-pipe operator
 #'
-#' See \code{\link[magrittr]{\\\%>\\\%}}.
+#' See \code{\link[magrittr]{\%>\%}}.
 #' @name %>%
 #' @importFrom magrittr %>%
 #' @export %>%
 NULL
 
 #' magrittr compound assignment pipe operator
 #'
-#' See \code{\link[magrittr]{\\\%<>\\\%}}.
+#' See \code{\link[magrittr]{\%<>\%}}.
 #' @name %<>%
 #' @importFrom magrittr %<>%
 #' @export %<>%

R/term_matching_functions.R

@@ -9,7 +9,7 @@
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' flat_json <- flatten_json(json)
 #'
@@ -46,7 +46,7 @@ match_terms <- function(flat_json, term_matching_table)
 #' data <- system.file(
 #'    file.path('extdata', 'testfile.raw'),
 #'    package = 'MARMoSET', mustWork = TRUE)
-#' json <- use_rawMetaAsJson(data)
+#' json <- generate_json(data)
 #'
 #' flat_json <- flatten_json(json)
 #'

README.Rmd

@@ -43,11 +43,11 @@ remotes::install_github('loosolab/MARMoSET', host='github.molgen.mpg.de/api/v3')
 
 ## Usage:
 
-The c# command line tool can be used in R with `use_rawMetaAsJson()` to create a JSON file including only the meta data of grouped raw files. It takes as argument `path_data`, a path to a raw file or a directory containing raw files.
+The c# command line tool can be used in R with `generate_json()` to create a JSON file including only the meta data of grouped raw files. It takes as argument `path_data`, a path to a raw file or a directory containing raw files.
 
-This JSON file can also be created by using the rawMetaAsJson.exe externally.
+This JSON file can also be created by using the MARMoSET.exe externally.
 
-Due to the design of the RawFileReader the rawMetaAsJson.exe and therefore this command is running as 64 bit code on Windows only. To use this package with another operating system, it is necessarry to already have the JSON file created.
+Due to the design of the RawFileReader the MARMoSET.exe and therefore this command is running as 64 bit code on Windows only. To use this package with another operating system, it is necessarry to already have the JSON file created. To open a JSON file in R the package `jsonlite` provides the function `fromJSON()`.
 
 ```{r}
 library(MARMoSET)
@@ -59,7 +59,7 @@ if(.Platform$OS.type == 'windows')
       file.path('extdata', 'testfile.raw'),
       package = 'MARMoSET', mustWork = TRUE)
   
-  json <- use_rawMetaAsJson(path_data = data)
+  json <- generate_json(path_data = data)
 } else
 {
   # non windows user need to read in the JSON file here

README.md

@@ -36,11 +36,11 @@ remotes::install_github('loosolab/MARMoSET', host='github.molgen.mpg.de/api/v3')
 Usage:
 ------
 
-The c\# command line tool can be used in R with `use_rawMetaAsJson()` to create a JSON file including only the meta data of grouped raw files. It takes as argument `path_data`, a path to a raw file or a directory containing raw files.
+The c\# command line tool can be used in R with `generate_json()` to create a JSON file including only the meta data of grouped raw files. It takes as argument `path_data`, a path to a raw file or a directory containing raw files.
 
-This JSON file can also be created by using the rawMetaAsJson.exe externally.
+This JSON file can also be created by using the MARMoSET.exe externally.
 
-Due to the design of the RawFileReader the rawMetaAsJson.exe and therefore this command is running as 64 bit code on Windows only. To use this package with another operating system, it is necessarry to already have the JSON file created.
+Due to the design of the RawFileReader the MARMoSET.exe and therefore this command is running as 64 bit code on Windows only. To use this package with another operating system, it is necessarry to already have the JSON file created. To open a JSON files in R the package `jsonlite` provides the function `fromJSON()`.
 
 ``` r
 library(MARMoSET)
@@ -52,7 +52,7 @@ if(.Platform$OS.type == 'windows')
       file.path('extdata', 'testfile.raw'),
       package = 'MARMoSET', mustWork = TRUE)
 
-  json <- use_rawMetaAsJson(path_data = data)
+  json <- generate_json(path_data = data)
 } else
 {
   # non windows user need to read in the JSON file here

inst/bin/rawMetaAsJson.exe.config → inst/bin/MARMoSET.exe.config

@@ -1,6 +1,6 @@
-<?xml version="1.0" encoding="utf-8" ?>
-<configuration>
-    <startup> 
-        <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.6.1" />
-    </startup>
+<?xml version="1.0" encoding="utf-8" ?>
+<configuration>
+    <startup> 
+        <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.6.1" />
+    </startup>
 </configuration>