Finish Release-1.2

.Rbuildignore

@@ -8,3 +8,4 @@ man-roxygen
 ^docs$
 ^pkgdown$
 ^\.github$
+^vignettes/articles$

DESCRIPTION

@@ -1,16 +1,15 @@
 Package: arcMS
 Type: Package
 Title: MS converter from UNIFI to Parquet and HDF5 formats
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: c(
  person("Julien", "Le Roux", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0245-8536")),
  person("Julien", "Sade", email = "[email protected]", role = "aut")
  )
 Maintainer: Julien Le Roux <[email protected]>
-Description: Functions to connect to Waters UNIFI API and convert data to parquet or HDF5 format.
+Description: Functions to connect to Waters UNIFI API and convert data to Parquet or HDF5 format.
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 RoxygenNote: 7.3.1
 Suggests:
  testthat (>= 3.0.0),
@@ -22,7 +21,10 @@ Suggests:
  shiny,
  bs4Dash,
  knitr,
- rmarkdown
+ rmarkdown,
+ duckdb,
+ plotly,
+ fontawesome
 Config/testthat/edition: 3
 Imports:
  methods,

NAMESPACE

@@ -14,18 +14,18 @@ export(get_sample_infos)
 export(get_samples_list)
 export(run_app)
 export(sample_dataset)
-export(sample_dataset_ondisk)
 export(sample_infos)
 export(save_one_sample_data)
 export(store_unifi_api_token)
 exportClasses(connection_params)
 exportClasses(sample_dataset)
-exportClasses(sample_dataset_ondisk)
 exportClasses(sample_infos)
+exportMethods(add_sample_id)
 exportMethods(connection_apihosturl)
 exportMethods(connection_token)
 exportMethods(get_analysis_name)
 exportMethods(get_sample_data)
+exportMethods(get_sample_id)
 exportMethods(get_sample_metadata)
 exportMethods(get_sample_metadata_json)
 exportMethods(get_sample_name)
@@ -38,10 +38,12 @@ import(methods)
 import(withr)
 importFrom(RProtoBuf,readProtoFiles)
 importFrom(Rcpp,evalCpp)
+importFrom(arrow,open_dataset)
 importFrom(arrow,read_parquet)
 importFrom(arrow,write_parquet)
 importFrom(checkmate,makeAssertion)
 importFrom(checkmate,vname)
+importFrom(dplyr,collect)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
 importFrom(future,multisession)

R/convert_bin_to_ccs.R

@@ -1,4 +1,5 @@
 #' Convert bin value to CCS (Collision Cross Section) value
+#'
 #' This function converts bin values to CCS values for the given sample.
 #' This conversion should be performed for a limited number of detected peaks
 #' and not on raw data to avoid too many requests and useless CCS calculations
@@ -20,11 +21,10 @@
 
 convert_bin_to_ccs <- function(sample_dataset, connection_params = NULL) {
  # Check if sample_id is accessible
- sample_metadata = get_sample_metadata(sample_dataset)
- if (!"id" %in% names(sample_metadata)) {
- stop("Sample ID is missing.")
+ sample_id = get_sample_id(sample_dataset)
+ if (is.null(sample_id)) {
+ stop("Sample ID is missing in sample_metadata. \nPlease add the sample ID to the sample_dataset object with the add_sample_id() method if needed.")
  }
- sample_id <- sample_metadata$id
 
  # Check connection parameters
  if (is.null(connection_params)) {
@@ -39,6 +39,14 @@ convert_bin_to_ccs <- function(sample_dataset, connection_params = NULL) {
  }
 
  sample_data = get_sample_data(sample_dataset)
+ # check if sample_data is Arrow pointer or data.table in RAM
+ if (inherits(sample_data, "FileSystemDataset")) {
+ sample_data = sample_data |> collect()
+ attr(sample_data, "sample_metadata") = NULL
+ attr(sample_data, "spectrum_metadata") = NULL
+ attr(sample_data, "sample_metadata_json") = NULL
+ attr(sample_data, "spectrum_metadata_json") = NULL
+ }
 
  # Change rt column name if necessary
  if ("retention_time" %in% names(sample_data)) {
@@ -61,21 +69,23 @@ convert_bin_to_ccs <- function(sample_dataset, connection_params = NULL) {
  charges = rep(1, nrow(sample_data)),
  retentiontimes = sample_data$rt
  ))
+ message(glue::glue("Requesting conversion of bin values to CCS to the UNIFI API..."))
 
  # Make API call
- response <- httr::POST(
- url = sampleUrl,
- body = body,
- httr::add_headers(
- "Content-Type" = "application/json",
- "Authorization" = paste("Bearer", token)
+ response <- httr::POST(
+ url = sampleUrl,
+ body = body,
+ httr::add_headers(
+ "Content-Type" = "application/json",
+ "Authorization" = paste("Bearer", token)
+ )
  )
- )
 
  # Check the response status
  if (httr::status_code(response) != 200) {
  stop("Error in API request: ", httr::content(response, "text", encoding = "UTF-8"))
  }
+ message(glue::glue("Conversion done."))
 
  # Update data with CCS values
  ccs_values <- jsonlite::fromJSON(httr::content(response, "text", encoding = "UTF-8"))

R/generics.R

@@ -2,8 +2,10 @@ setGeneric("connection_apihosturl", function(obj, ...) standardGeneric("connecti
 setGeneric("connection_token", function(obj, ...) standardGeneric("connection_token"))
 setGeneric("get_sample_metadata", function(obj, ...) standardGeneric("get_sample_metadata"))
 setGeneric("get_sample_name", function(obj, ...) standardGeneric("get_sample_name"))
+setGeneric("get_sample_id", function(obj, ...) standardGeneric("get_sample_id"))
 setGeneric("get_analysis_name", function(obj, ...) standardGeneric("get_analysis_name"))
 setGeneric("get_sample_metadata_json", function(obj, ...) standardGeneric("get_sample_metadata_json"))
 setGeneric("get_spectrum_metadata", function(obj, ...) standardGeneric("get_spectrum_metadata"))
 setGeneric("get_spectrum_metadata_json", function(obj, ...) standardGeneric("get_spectrum_metadata_json"))
 setGeneric("get_sample_data", function(obj, ...) standardGeneric("get_sample_data"))
+setGeneric("add_sample_id", function(obj, id, ...) standardGeneric("add_sample_id"))

R/main.R

@@ -7,7 +7,7 @@
 #' @importFrom utils head tail modifyList setTxtProgressBar txtProgressBar write.csv write.table read.csv data getFromNamespace
 #' @importFrom stats ave
 #' @importFrom magrittr %>%
-#' @importFrom dplyr mutate select
+#' @importFrom dplyr mutate select collect
 #' @importFrom tidytable uncount unnest
 #' @importFrom RProtoBuf readProtoFiles
 #' @importFrom httr GET add_headers content POST
@@ -16,7 +16,7 @@
 #' @importFrom future plan multisession
 #' @importFrom future.apply future_lapply
 #' @importFrom progressr progressor with_progress withProgressShiny
-#' @importFrom arrow write_parquet read_parquet
+#' @importFrom arrow write_parquet read_parquet open_dataset
 #' @importFrom rhdf5 h5write h5createFile
 NULL # need this for doc generation
 
@@ -47,5 +47,6 @@ NULL
 #'
 "_PACKAGE"
 NULL
-
+setOldClass("FileSystemDataset")
 setClassUnion("dataframeOrDatatable", c("data.frame", "data.table"))
+setClassUnion("dataframeOrDatatableOrArrowdataset", c("data.frame", "data.table", "FileSystemDataset"))