Finish Release-1.2.1

leesulab · Oct 3, 2024 · 2181384 · 2181384
2 parents 2719d1a + 117d156
commit 2181384
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Showing 4 changed files with 9 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -10,7 +10,7 @@ Maintainer: Julien Le Roux <[email protected]>
 Description: Functions to connect to Waters UNIFI API and convert data to Parquet or HDF5 format.
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests:
  testthat (>= 3.0.0),
  spsComps,

diff --git a/R/convert_one_sample_data.R b/R/convert_one_sample_data.R
@@ -38,9 +38,9 @@ convert_one_sample_data <- function(sample_id, connection_params = NULL, format
  message(glue::glue("File '{sample_name}' already exists..."))
  } else {
  collected_data = collect_one_sample_data(sample_id, connection_params, num_spectras)
- printf("Start Saving")
+ # printf("Start Saving")
  save_one_sample_data(collected_data, sample_name, analysis_name, path = path, format = format)
- printf("End Saving")
+ # printf("End Saving")
  rm(collected_data)
  }
  }

diff --git a/inst/shiny-app/server.R b/inst/shiny-app/server.R
@@ -50,7 +50,7 @@ server <- function(input, output, session) {
 
  analysisList <- shiny::eventReactive(input$jstreefolders_selected, {
  req(input$jstreefolders_selected)
- print(input$jstreefolders_selected)
+ # print(input$jstreefolders_selected)
  if(length(input$jstreefolders_selected) != 0) {
  df = rv$folders
  selfolder = input$jstreefolders_selected[[1]]$text
@@ -136,8 +136,9 @@ server <- function(input, output, session) {
  progressr::withProgressShiny(message = "Conversion in progress", {
  spsComps::shinyCatch({
  #sampleId = "0134efbf-c75a-411b-842a-4f35e2b76347"
- collected_data = arcMS::collect_one_sample_data(sampleId, rv$con)
- arcMS::save_one_sample_data(collected_data, path = shinyFiles::parseDirPath(c(home = '~'), selected_dir()), format = format)
+ arcMS::convert_one_sample_data(sampleId, rv$con, format = format, path = shinyFiles::parseDirPath(c(home = '~'), selected_dir()), overwrite = input$overwrite)
+ # collected_data = arcMS::collect_one_sample_data(sampleId, rv$con)
+ # arcMS::save_one_sample_data(collected_data, path = shinyFiles::parseDirPath(c(home = '~'), selected_dir()), format = format)
  },
  prefix = "", blocking_level = "error"
  )
@@ -161,7 +162,7 @@ server <- function(input, output, session) {
  if(input$fileFormat == 1) format = "parquet" else format = "hdf5"
  progressr::withProgressShiny(message = "Conversion in progress", {
  spsComps::shinyCatch({
- arcMS::convert_all_samples_data(analysisId, rv$con, format = format, path = shinyFiles::parseDirPath(c(home = '~'), selected_dir()))
+ arcMS::convert_all_samples_data(analysisId, rv$con, format = format, path = shinyFiles::parseDirPath(c(home = '~'), selected_dir()), overwrite = input$overwrite)
  },
  prefix = "", blocking_level = "error"
  )

diff --git a/inst/shiny-app/ui.R b/inst/shiny-app/ui.R
@@ -98,6 +98,7 @@ ui <- bs4Dash::dashboardPage(skin = "blue",
  align = "center"
  )
  ),
+ shiny::checkboxInput(inputId = "overwrite", label = "Overwrite files if already present in selection directory?", value = FALSE),
  shiny::actionButton(inputId = "convert_one", label = "Convert one sample selected in the Samples table"),
  shiny::actionButton(inputId = "convert_all", label = "Convert all samples from the selected Analysis"),
  shiny::textOutput("conversion_end_message")