fix tests

DESCRIPTION

@@ -42,7 +42,7 @@ Imports:
  R.utils (>= 2.12.3),
  rlang (>= 1.1.4),
  rotl (>= 3.1.0),
- shiny (>= 1.9.0),
+ shiny (>= 1.9.1),
  shinybusy (>= 0.3.3),
  shinyhelper (>= 0.3.2),
  shinyjs (>= 2.1.0),
@@ -134,7 +134,6 @@ Collate:
  'globals.R'
  'harmonize_names_sirius.R'
  'harmonize_spectra.R'
- 'import-standalone-purrr.R'
  'install.R'
  'load_yaml_files.R'
  'log_debug.R'

NAMESPACE

@@ -99,9 +99,7 @@ importFrom(Spectra,filterEmptySpectra)
 importFrom(Spectra,filterFourierTransformArtefacts)
 importFrom(Spectra,filterIntensity)
 importFrom(Spectra,filterPrecursorCharge)
-importFrom(Spectra,peaksData)
 importFrom(Spectra,reduceSpectra)
-importFrom(Spectra,spectraData)
 importFrom(crayon,blue)
 importFrom(crayon,cyan)
 importFrom(crayon,green)

R/extract_spectra.R

@@ -1,28 +1,22 @@
-import::from(Spectra, peaksData, .into = environment())
-import::from(Spectra, spectraData, .into = environment())
 import::from(tidytable, across, .into = environment())
 import::from(tidytable, any_of, .into = environment())
 import::from(tidytable, as_tidytable, .into = environment())
 import::from(tidytable, everything, .into = environment())
 import::from(tidytable, group_by, .into = environment())
 import::from(tidytable, mutate, .into = environment())
-import::from(tidytable, reframe, .into = environment())
 import::from(tidytable, rename, .into = environment())
 import::from(tidytable, select, .into = environment())
 
 #' @title Extract spectra from a Spectra object
 #'
 #' @description This function extracts spectra from a `Spectra`object
 #'
-#' @importFrom Spectra peaksData
-#' @importFrom Spectra spectraData
 #' @importFrom tidytable across
 #' @importFrom tidytable any_of
 #' @importFrom tidytable as_tidytable
 #' @importFrom tidytable everything
 #' @importFrom tidytable group_by
 #' @importFrom tidytable mutate
-#' @importFrom tidytable reframe
 #' @importFrom tidytable rename
 #' @importFrom tidytable select
 #'
@@ -44,23 +38,18 @@ extract_spectra <- function(object) {
  incoherent_integer <- c("spectrum_id")
  incoherent_numeric <- c("PrecursorMZ")
 
- ## Extract peaks data and transform it into a data frame
- peaks <- object |>
- peaksData() |>
- data.frame() |>
- as_tidytable() |>
- group_by(group) |>
- reframe(across(.cols = everything(), .fns = list))
-
  ## Extract spectra data and transform it into a data frame
- spectra <- object |>
- spectraData() |>
+ spectra <- object@backend@spectraData |>
  data.frame() |>
  as_tidytable()
 
  ## Add 'mz' and 'intensity' columns from peaks data
- spectra$mz <- peaks$mz
- spectra$intensity <- peaks$intensity
+ spectra$mz <- lapply(object@backend@peaksData, function(peakData) {
+ peakData[, 1]
+ })
+ spectra$intensity <- lapply(object@backend@peaksData, function(peakData) {
+ peakData[, 2]
+ })
 
  ## Synonyms issue
  # spectra <- spectra |>

R/harmonize_spectra.R

@@ -47,25 +47,25 @@ import::from(tidytable, select, .into = environment())
 #'
 #' @examples NULL
 harmonize_spectra <- function(spectra,
- metad = get("metad", envir = parent.frame()),
+ metad,
  mode,
- col_ad = get("col_ad", envir = parent.frame()),
- col_ce = get("col_ce", envir = parent.frame()),
- col_ci = get("col_ci", envir = parent.frame()),
- col_em = get("col_em", envir = parent.frame()),
- col_in = get("col_in", envir = parent.frame()),
- col_io = get("col_io", envir = parent.frame()),
- col_ik = get("col_ik", envir = parent.frame()),
- col_il = get("col_il", envir = parent.frame()),
- col_mf = get("col_mf", envir = parent.frame()),
- col_na = get("col_na", envir = parent.frame()),
- col_po = get("col_po", envir = parent.frame()),
- col_sm = get("col_sm", envir = parent.frame()),
- col_sn = get("col_sn", envir = parent.frame()),
- col_si = get("col_si", envir = parent.frame()),
- col_sp = get("col_sp", envir = parent.frame()),
- col_sy = get("col_sy", envir = parent.frame()),
- col_xl = get("col_xl", envir = parent.frame())) {
+ col_ad,
+ col_ce,
+ col_ci,
+ col_em,
+ col_in,
+ col_io,
+ col_ik,
+ col_il,
+ col_mf,
+ col_na,
+ col_po,
+ col_sm,
+ col_sn,
+ col_si,
+ col_sp,
+ col_sy,
+ col_xl) {
  columns <- c(
  "adduct",
  "collision_energy",
@@ -141,7 +141,7 @@ harmonize_spectra <- function(spectra,
  mz,
  intensity
  ) |>
- mutate(join = "x")
+ bind_cols(tidytable(join = "x"))
 
  spectra_harmonized <- spectra_filtered |>
  full_join(spectra_missing) |>