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DESCRIPTION

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+Package: MARMoSET
+Type: Package
+Title: Get metadata out of raw files
+Version: 0.1.0
+Author: Who wrote it
+Maintainer: The package maintainer <yourself@somewhere.net>
+Description: This packages uses a c# command line tool to extract the meta data of a raw file into a json file.
+    It contains methods to collect data requred for publication by journal and to write them into a tab delimited text file. 
+License: What license is it under?
+Encoding: UTF-8
+LazyData: true
+Imports:
+    assertive.base,
+    assertive.files,
+    assertive.numbers,
+    assertive.properties,
+    assertive.reflection,
+    assertive.sets,
+    assertive.strings,
+    assertive.types,
+    jsonlite,
+    pathological,
+    rlist,
+    stringi,
+    magrittr
+Depends:
+    R (>= 2.10)
+Suggests:
+    readODS,
+    knitr,
+    rmarkdown
+RoxygenNote: 6.1.1
+VignetteBuilder: knitr

MARMoSET.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export("%<>%")
+export("%>%")
+export(create_term_match_table)
+export(files_in_group)
+export(flatten_json)
+export(gradient_tables)
+export(group_count)
+export(instrument_names)
+export(match_terms)
+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

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+#' Number of groups in the json file
+#'
+#' @param json A JSON file generated by the function "use_rawMetaAsJson()" or by using rawMetaAsJson.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)
+#'
+#' group_count(json)
+#'
+#' @export
+
+group_count <- function(json)
+{
+  assertive.types::assert_is_list(json)
+
+  return(json[["Group"]] %>% length())
+}
+
+
+#' Filenames of one group
+#'
+#' @param json A JSON file generated by the function "use_rawMetaAsJson()" or by using rawMetaAsJson.exe externaly.
+#' @param group_number An index that determines the group.
+#'
+#' @return A list of filenames belonging to the choosen group.
+#'
+#' @examples
+#' data <- system.file(
+#'    file.path('extdata', 'testfile.raw'),
+#'    package = 'MARMoSET', mustWork = TRUE)
+#' json <- use_rawMetaAsJson(data)
+#'
+#' files_in_group(json, 1)
+#'
+#' @export
+
+files_in_group <- function(json, group_number)
+{
+  assertive.types::assert_is_list(json)
+  assertive.types::assert_is_a_number(group_number)
+  assertive.numbers::assert_all_are_less_than_or_equal_to(group_number, group_count(json))
+
+  return(json[["Group"]][[group_number]][["Names"]])
+}
+
+
+#' Get instrument names
+#'
+#' @param json A JSON file generated by the function "use_rawMetaAsJson()" or by using rawMetaAsJson.exe externaly.
+#' @param group_number An index that determines the group.
+#'
+#' @return A list of instruments used in the choosen group.
+#'
+#' @examples
+#' data <- system.file(
+#'    file.path('extdata', 'testfile.raw'),
+#'    package = 'MARMoSET', mustWork = TRUE)
+#' json <- use_rawMetaAsJson(data)
+#'
+#' instrument_names(json, 1)
+#'
+#' @export
+
+instrument_names <- function(json, group_number)
+{
+  assertive.types::assert_is_list(json)
+  assertive.types::assert_is_a_number(group_number)
+  assertive.numbers::assert_all_are_less_than_or_equal_to(group_number, group_count(json))
+
+  instruments <- json[["Group"]][[group_number]][["Instruments"]] %>%
+                  summary() %>%
+                  rownames()
+
+  return(instruments)
+}

R/data.R

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+#' Term matching tables for different instruments
+#'
+#'
+#'
+#' @format A list of data frames:
+#' \describe{
+#'   \item{Q_Exactive_Plus_-_Orbitrap_MS}{MS instrument}
+#'   \item{Q_Exactive_HF_-_Orbitrap_MS}{MS instrument}
+#'   \item{Q_Exactive_-_Orbitrap_MS}{MS instrument}
+#'   \item{Thermo_EASY-nLC}{LC pump}
+#'   ...
+#' }
+"tmt_list"

R/gradient_functions.R

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+#' Gradient table to string.
+#'
+#' @param flat_json A flattened JSON file, created by "prepare_json()".
+#' @param group_number An index that determines the group.
+#'
+#' @return Gradient information as sentence.
+
+gradient_as_string <- function(flat_json, group_number)
+{
+  assertive.types::assert_is_list(flat_json)
+  assertive.types::assert_is_a_number(group_number)
+
+  grad_tab <- one_gradient_table(flat_json, group_number)
+  grad_tab$`Duration[mm:ss]` %<>%
+    stringi::stri_replace_all_regex(pattern =  ":.*", replacement = "") %<>%
+    stringi::stri_replace_all_regex(pattern =  "^0", replacement = "")
+
+
+  if(dim(table(grad_tab$`Flow[nl/min]`)) == 1)
+  {
+    flow <- paste("The flow is consistently at", grad_tab$`Flow[nl/min]`[1],"nl/min.",
+                  sep = " ")
+  } else
+  {
+    flow <- paste("The flow is ranging from ", min(grad_tab$`Flow[nl/min]`),
+                  " to ",  max(grad_tab$`Flow[nl/min]`," nl/min."),
+                  sep = "")
+  }
+
+  first <- paste("The quantity of B in percent is from ", grad_tab$`Mixture[%B]`[1], "% B in ",
+        grad_tab$`Duration[mm:ss]`[2], " minutes to ",
+        grad_tab$`Mixture[%B]`[2], "% B.",
+        sep = "")
+
+  following <- paste("In ", grad_tab$`Duration[mm:ss]`[3:nrow(grad_tab)], " minutes to ",
+        grad_tab$`Mixture[%B]`[3:nrow(grad_tab)], "% B.", sep = "", collapse = " ")
+
+  paste(flow, first, following,  sep=" ") %>%
+    return()
+}
+
+#' Gradient.
+#'
+#' @param flat_json A flattened JSON file, created by "prepare_json()".
+#' @param group_number An index that determines the group.
+#' @param lc_pump Name of the used lc_pump, default = "Thermo EASY-nLC".
+#'
+#' @return A table with gradient.
+#'
+#' @examples
+#' data <- system.file(
+#'    file.path('extdata', 'testfile.raw'),
+#'    package = 'MARMoSET', mustWork = TRUE)
+#' json <- use_rawMetaAsJson(data)
+#'
+#' flat_json <- flatten_json(json)
+#'
+#' one_gradient_table(flat_json, 1)
+#'
+#' @export
+
+one_gradient_table <- function(flat_json, group_number, lc_pump = "Thermo EASY-nLC")
+{
+  assertive.types::assert_is_list(flat_json)
+  assertive.types::assert_is_a_number(group_number)
+  assertive.properties::assert_is_not_null(flat_json[[paste("Group" , group_number , "Instruments", lc_pump, "InstrumentFriendName", sep = ".")]])
+
+  time <- flat_json[[paste0("Group.",group_number,".Instruments.Thermo EASY-nLC.Method.Gradient.Time [mm:ss]")]]
+  duration <- flat_json[[paste0("Group.",group_number,".Instruments.Thermo EASY-nLC.Method.Gradient.Duration [mm:ss]")]]
+  flow <- flat_json[[paste0("Group.",group_number,".Instruments.Thermo EASY-nLC.Method.Gradient.Flow [nl/min]")]]
+  mixture <- flat_json[[paste0("Group.",group_number,".Instruments.Thermo EASY-nLC.Method.Gradient.Mixture [%B]")]]
+
+  gradient_tab <- data.frame(
+   "Time[mm:ss]" = time,
+   "Duration[mm:ss]" = duration,
+   "Flow[nl/min]" = flow,
+   "Mixture[%B]" = mixture,
+   check.names = FALSE,
+   stringsAsFactors = FALSE)
+
+  return(gradient_tab)
+}
+
+
+#' Create a list with all gradient tables.
+#'
+#' @param flat_json A flattened JSON file, created by "prepare_json()".
+#' @param lc_pump Name of the used lc pump, default = "Thermo EASY-nLC"
+#'
+#' @return List of gradients for all groups
+#'
+#' @examples
+#' data <- system.file(
+#'    file.path('extdata', 'testfile.raw'),
+#'    package = 'MARMoSET', mustWork = TRUE)
+#' json <- use_rawMetaAsJson(data)
+#'
+#' flat_json <- flatten_json(json)
+#'
+#' gradient_tables(flat_json)
+#'
+#' @export
+
+gradient_tables <- function(flat_json, lc_pump = "Thermo EASY-nLC")
+{
+  assertive.types::assert_is_list(flat_json)
+  assertive.types::assert_is_a_string(lc_pump)
+
+  group_count <- flat_json %>% names() %>% stringi::stri_extract_first_regex('^Group\\.\\d+\\.') %>% table() %>% length()
+
+  vector_of_gradient_tables <- lapply(1:group_count, function(group) one_gradient_table(flat_json, group, lc_pump))
+
+  return(vector_of_gradient_tables)
+}

R/load_meta_functions.R

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+#' create a JSON File
+#'
+#' @param path_data Path to raw file or directory containing raw files.
+#'
+#' @return JSON object containing the meta data of the raw files.
+#'
+#' @examples
+#' data <- system.file(
+#'    file.path('extdata', 'testfile.raw'),
+#'    package = 'MARMoSET', mustWork = TRUE)
+#' json <- use_rawMetaAsJson(data)
+#'
+#' @export
+
+use_rawMetaAsJson <- function(path_data)
+{
+  new_file <- tempfile()
+  path_rawMetaAsJson <- system.file(
+    file.path('bin','rawMetaAsJson.exe'),
+    package = 'MARMoSET', mustWork = TRUE)
+
+  assertive.files::assert_all_are_executable_files(path_rawMetaAsJson, 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,
+                                 msg = "path_data is not a file or directory!",
+                                 severity = "stop",
+                                 what = "any")
+
+  if(!assertive.reflection::is_windows())
+  {
+    stop("Function is only working under windows.")
+  }
+
+  system(command = paste(path_rawMetaAsJson, paste0('"',path_data, '"'), new_file),
+         intern  = T)
+
+  json <- jsonlite::fromJSON(new_file)
+
+  return(json)
+}
+
+
+#' flattening JSON
+#'
+#' @param json A JSON file generated by the function "use_rawMetaAsJson()" or by using rawMetaAsJson.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)
+#'
+#' flat_json <- flatten_json(json)
+#'
+#' @export
+
+flatten_json <- function(json)
+{
+  assertive.types::assert_is_list(json)
+
+  return(json %>% rlist::list.flatten())
+}