Nothing
R/FilteringServerLogic.R
In inDAGO: A GUI for Dual and Bulk RNA-Sequencing Analysis
Defines functions
FilteringServerLogic
Documented in
FilteringServerLogic
#' Server function for filtering module in Shiny application
#' @param id Shiny module identifier
FilteringServerLogic <- function(id) {
shiny::moduleServer(id, function(input, output, session) {
#Pre-processing
# Define available directories for file selection
volumes <- c(Home = fs::path_home(),
"R Installation" = R.home(),
shinyFiles::getVolumes()())
# Filtering: Allow user to select the directory for raw reads
shinyFiles::shinyDirChoose(
input,
"directoryRawReadsFilteringUpload",
roots = volumes,
session = session,
restrictions = system.file(package = "base"),
allowDirCreate = FALSE
)
# Observe directory selection and print to console
shiny::observe({
cat("\ninput$directoryRawReadsFilteringUpload value:\n\n")
print(input$directoryRawReadsFilteringUpload)
})
# Reactive value to store the filtering upload path
dirFilteringUploadPath <- shiny::reactiveVal()
shiny::observe({
dir <- shinyFiles::parseDirPath(volumes, input$directoryRawReadsFilteringUpload)
dirFilteringUploadPath(dir)
})
# Output the selected directory path for the raw reads
output$DirFilteringUploadPath <- shiny::renderPrint({
if (is.integer(input$directoryRawReadsFilteringUpload)) {
cat("No directory has been selected")
} else {
shinyFiles::parseDirPath(volumes, input$directoryRawReadsFilteringUpload)
}
})
# Filtering: Allow user to select the directory for filtered output
shinyFiles::shinyDirChoose(
input,
"directoryRawReadsFilteredDownload",
roots = volumes,
session = session,
restrictions = system.file(package = "base"),
allowDirCreate = FALSE
)
# Observe directory selection and print to console
shiny::observe({
cat("\ninput$directoryRawReadsFilteredDownload value:\n\n")
print(input$directoryRawReadsFilteredDownload)
})
# Reactive value to store the filtering download path
dirFilteringDownloadPath <- shiny::reactiveVal()
shiny::observe({
dir <- shinyFiles::parseDirPath(volumes, input$directoryRawReadsFilteredDownload)
dirFilteringDownloadPath(dir)
})
# Output the selected directory path for the filtered output
output$DirFilteringDownloadPath <- shiny::renderPrint({
if (is.integer(input$directoryRawReadsFilteredDownload)) {
cat("No directory has been selected")
} else {
shinyFiles::parseDirPath(volumes, input$directoryRawReadsFilteredDownload)
}
})
# List files in the raw reads directory and prepare filtering options
ListFIlter <- shiny::reactiveVal()
shiny::observe({
shiny::req(dirFilteringUploadPath())
l <- list.files(dirFilteringUploadPath(),
"*fastq$|*fq$|*fastq.gz$|*fq.gz$")
Sample <- sub(
'_1.fastq|_1.fq|_1.fastq.gz|_1.fq.gz|_2.fastq|_2.fq|_2.fastq.gz|_2.fq.gz',
"",
l
) %>% unique(.)
gr <- function(x) {
l[grep(x, l)]
}
listFilter <- lapply(Sample, gr)
ListFIlter(listFilter)
})
# shiny::reactiveVal to save execution time
start_time_filtering <- shiny::reactiveVal()
# shiny::reactiveVal to save path for temporary files
logFile <- shiny::reactiveVal()
# Reactive value to store Filtering_process
rvFil <- shiny::reactiveValues()
# Run the filtering process in a background
shiny::observeEvent(input$Filtering, {
# Check if directories are selected
if (is.integer(input$directoryRawReadsFilteringUpload) ||
is.integer(input$directoryRawReadsFilteredDownload)) {
shiny::showNotification(
"Please select all required input in 'Step 1 - Set input/output'",
closeButton = TRUE,
duration = 10,
type = "error"
)
} else {
if (length(list.files(
dirFilteringDownloadPath(),
"*fastq$|*fq$|*fastq.gz$|*fq.gz$"
)) > 1) {
} else {
#start time to monitor execution
start_time_filtering(Sys.time())
shinyjs::disable("Filtering")
shinyjs::enable("killFiltering")
tryCatch({
rvFil$Filtering_process <- callr::r_bg(
func = Filtering
,
args = list(
Nodes = input$filteringThreads,
X = ListFIlter(),
UploadPath = file.path(dirFilteringUploadPath(), "/"),
DownloadPath = file.path(dirFilteringDownloadPath(), "/"),
qualityType = input$QualityTypeFiltering,
minLen = input$minLen,
trim = input$trim,
trimValue = input$trimValue,
n = input$nChunk,
Adapters = input$Adapters,
Lpattern = input$Lpattern,
Rpattern = input$Rpattern,
max.Lmismatch = input$max.Lmismatch,
max.Rmismatch = input$max.Rmismatch,
kW = input$kW,
left = input$left,
right = input$right,
halfwidthAnalysis = input$halfwidthAnalysis,
halfwidth = input$halfwidth,
compress = input$compress
)
,
supervise = TRUE
,
error = getOption("callr.error", "error")
)
}
, error = function(e) {
shiny::showNotification(
"error occours - check if files with the name of the samples already exist in selected folder",
action = NULL,
duration = NULL,
closeButton = TRUE,
id = NULL,
type = "error"
)
}) # End of tryCatch
shiny::showNotification(
"Filtering analysis has been started",
action = NULL,
duration = 10,
closeButton = TRUE,
id = NULL,
type = "message"
)
}
}
})
# Output the status of the filtering process
shiny::observeEvent(input$Filtering, {
if (is.integer(input$directoryRawReadsFilteringUpload) ||
is.integer(input$directoryRawReadsFilteredDownload)) {
# No action needed if directories are not selected
} else {
if (length(list.files(
dirFilteringDownloadPath(),
"*fastq$|*fq$|*fastq.gz$|*fq.gz$"
)) > 1) {
} else {
output$CheckStatusOut <- shiny::renderPrint({
shiny::req(input$Filtering)
if (shiny::isolate(rvFil$Filtering_process$is_alive()) == TRUE) {
# autoInvalidate()
shiny::invalidateLater(5000)
rvFil$Filtering_process$print()
cat(
shiny::isolate(
"This process could be time-consuming\nFeel free to take a coffee break\n\n ( (\n ) )\n ..........\n | |]\n \\ /\n '----'"
)
)
} else {
#check end time of process
end_time_filtering <- Sys.time()
execution_time_filtering <- end_time_filtering - start_time_filtering()
# Convert to hours, minutes, and seconds
execution_time_sec_filtering <- as.numeric(execution_time_filtering, units="secs")
hours_filtering <- floor(execution_time_sec_filtering / 3600)
minutes_filtering <- floor((execution_time_sec_filtering %% 3600) / 60)
seconds_filtering <- execution_time_sec_filtering %% 60
# Print the result
cat(paste(shiny::isolate("The filtering analysis has been completed!\n")),"Execution Time: ", hours_filtering, "hours", minutes_filtering, "minutes", round(seconds_filtering, 2), "seconds\n")
# shinyjs::enable and shinyjs::disable button
shinyjs::enable("Filtering")
shinyjs::disable("killFiltering")
}
})
}
}
})
# Interrupt the filtering process if the kill button is clicked
shiny::observeEvent(input$killFiltering, {
# stop the slow Filtering() function
rvFil$Filtering_process$kill() #Terminate the process. It also terminate all of its child processes, except if they have created a new process group (on Unix), or job object (on Windows). It returns TRUE if the process was terminated, and FALSE if it was not (because it was already finished/dead when processx tried to terminate it).
shinyjs::enable("Filtering")
shinyjs::disable("killFiltering")
output$CheckStatusOut <- shiny::renderPrint({
shiny::invalidateLater(5000)
# autoInvalidate()
if (shiny::isolate(rvFil$Filtering_process$is_alive()) == FALSE) {
cat(shiny::isolate("The filtering analysis has been killed!"))
unlink(logFile())
}
})
shiny::showNotification(
"The filtering analysis has been killed!",
action = NULL,
duration = 10,
closeButton = TRUE,
id = NULL,
type = "warning"
)
})
shiny::observe({
# Check if the download directory is empty to avoid overwriting files
if (length(list.files(
dirFilteringDownloadPath(),
"*fastq$|*fq$|*fastq.gz$|*fq.gz$"
)) > 1) {
shiny::showNotification(
"The folder already contains FASTQ files - select an empty folder",
action = NULL,
duration = NULL,
closeButton = TRUE,
id = NULL,
type = "warning",
session = getDefaultReactiveDomain()
)
}
})
shiny::observeEvent(input$Filtering, {
shiny::req(dirFilteringUploadPath())
shiny::req(dirFilteringDownloadPath())
if (length(list.files(dirFilteringDownloadPath(), "*fastq$|*fq$|*fastq.gz$|*fq.gz$")) > 1) {
shiny::showNotification(
"The folder already contains FASTQ files - select an empty folder",
type = "error",
duration = NULL
)
} else {
# Reactive polling to check for new files
dataFiltering <- shiny::reactivePoll(
5000,
session,
checkFunc = function() {
files <- list.files(dirFilteringDownloadPath(), "*fastq$|*fq$|*fastq.gz$|*fq.gz$", full.names = TRUE)
if (length(files) > 0) {
return(max(file.info(files)$mtime))
}
return(Sys.time()) # Avoid NULL return
},
valueFunc = function() {
files <- list.files(dirFilteringDownloadPath(), "*fastq$|*fq$|*fastq.gz$|*fq.gz$", full.names = TRUE)
if (length(files) == 0) {
return(data.frame(
files = character(),
`size (gb)` = numeric(),
`mtime (y-m-d_h-m-s)` = character(),
Processed = numeric(),
Retained = numeric(),
Discarded = numeric(),
`Discarded_%` = character()
))
}
info <- file.info(files)
info$size <- info$size / 1e9
info$files <- basename(rownames(info))
info <- dplyr::select(info, c("files", "size", "mtime")) %>%
dplyr::rename(
"size (gb)" = "size",
"mtime (y-m-d_h-m-s)" = "mtime"
)
empty_df_with_na <- data.frame(
col1 = NA, # Column 1 (NA value)
col2 = NA, # Column 2 (NA value)
col3 = NA, # Column 3 (NA value)
col4 = NA # Column 4 (NA value)
)
info <- cbind(info,empty_df_with_na)
fileslog <- list.files(dirFilteringDownloadPath(), "*.log$", full.names = TRUE)
logFile(fileslog)
if (length(fileslog) > 0) {
resultSum <- sapply(fileslog, function(i) {
df <- utils::read.table(i)
name <- unique(df$V1)
processStats <- function(name) {
df1sum <- df %>% filter(V1 == name) %>% select(2:4) %>% apply(., 2, sum)
percentDiscarded <- paste0(round(as.numeric(df1sum[3]) * 100 / as.numeric(df1sum[1]), 2), "%")
return(c(name, df1sum, percentDiscarded))
}
df1 <- processStats(name[[1]])
df2 <- processStats(name[[2]])
df <- rbind(df1, df2) %>%
`colnames<-`(c("files", "Processed", "Retained", "Discarded", "Discarded_%"))
return(df)
}, simplify = FALSE, USE.NAMES = TRUE) %>% do.call(rbind, .)
info <- dplyr::left_join(info[1:3], data.frame(resultSum), by = "files")
}
return(info)
}
)
output$FilteredSample <- DT::renderDT(
dataFiltering(),
selection = 'none',
editable = FALSE,
rownames = FALSE,
colnames = c("files",
"size (gb)",
"mtime (y-m-d_h-m-s)",
"Processed",
"Retained",
"Discarded",
"Discarded_%"),
extensions = 'Buttons',
options = list(
paging = FALSE,
searching = TRUE,
fixedColumns = TRUE,
autoWidth = TRUE,
ordering = TRUE,
dom = 'Bfrtip',
buttons = list(
list(extend = 'csv', title = "FilteringResult")
)),
class = "display"
)
}
})
} # close function inside moduleServer
) # close moduleServer
} # close IndexingBulkServerLogic function
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inDAGO documentation built on Aug. 8, 2025, 7:47 p.m.
R Package Documentation
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Defines functions FilteringServerLogic
Documented in FilteringServerLogic
#' Server function for filtering module in Shiny application
#' @param id Shiny module identifier
FilteringServerLogic <- function(id) {
shiny::moduleServer(id, function(input, output, session) {
#Pre-processing
# Define available directories for file selection
volumes <- c(Home = fs::path_home(),
"R Installation" = R.home(),
shinyFiles::getVolumes()())
# Filtering: Allow user to select the directory for raw reads
shinyFiles::shinyDirChoose(
input,
"directoryRawReadsFilteringUpload",
roots = volumes,
session = session,
restrictions = system.file(package = "base"),
allowDirCreate = FALSE
)
# Observe directory selection and print to console
shiny::observe({
cat("\ninput$directoryRawReadsFilteringUpload value:\n\n")
print(input$directoryRawReadsFilteringUpload)
})
# Reactive value to store the filtering upload path
dirFilteringUploadPath <- shiny::reactiveVal()
shiny::observe({
dir <- shinyFiles::parseDirPath(volumes, input$directoryRawReadsFilteringUpload)
dirFilteringUploadPath(dir)
})
# Output the selected directory path for the raw reads
output$DirFilteringUploadPath <- shiny::renderPrint({
if (is.integer(input$directoryRawReadsFilteringUpload)) {
cat("No directory has been selected")
} else {
shinyFiles::parseDirPath(volumes, input$directoryRawReadsFilteringUpload)
}
})
# Filtering: Allow user to select the directory for filtered output
shinyFiles::shinyDirChoose(
input,
"directoryRawReadsFilteredDownload",
roots = volumes,
session = session,
restrictions = system.file(package = "base"),
allowDirCreate = FALSE
)
# Observe directory selection and print to console
shiny::observe({
cat("\ninput$directoryRawReadsFilteredDownload value:\n\n")
print(input$directoryRawReadsFilteredDownload)
})
# Reactive value to store the filtering download path
dirFilteringDownloadPath <- shiny::reactiveVal()
shiny::observe({
dir <- shinyFiles::parseDirPath(volumes, input$directoryRawReadsFilteredDownload)
dirFilteringDownloadPath(dir)
})
# Output the selected directory path for the filtered output
output$DirFilteringDownloadPath <- shiny::renderPrint({
if (is.integer(input$directoryRawReadsFilteredDownload)) {
cat("No directory has been selected")
} else {
shinyFiles::parseDirPath(volumes, input$directoryRawReadsFilteredDownload)
}
})
# List files in the raw reads directory and prepare filtering options
ListFIlter <- shiny::reactiveVal()
shiny::observe({
shiny::req(dirFilteringUploadPath())
l <- list.files(dirFilteringUploadPath(),
"*fastq$|*fq$|*fastq.gz$|*fq.gz$")
Sample <- sub(
'_1.fastq|_1.fq|_1.fastq.gz|_1.fq.gz|_2.fastq|_2.fq|_2.fastq.gz|_2.fq.gz',
"",
l
) %>% unique(.)
gr <- function(x) {
l[grep(x, l)]
}
listFilter <- lapply(Sample, gr)
ListFIlter(listFilter)
})
# shiny::reactiveVal to save execution time
start_time_filtering <- shiny::reactiveVal()
# shiny::reactiveVal to save path for temporary files
logFile <- shiny::reactiveVal()
# Reactive value to store Filtering_process
rvFil <- shiny::reactiveValues()
# Run the filtering process in a background
shiny::observeEvent(input$Filtering, {
# Check if directories are selected
if (is.integer(input$directoryRawReadsFilteringUpload) ||
is.integer(input$directoryRawReadsFilteredDownload)) {
shiny::showNotification(
"Please select all required input in 'Step 1 - Set input/output'",
closeButton = TRUE,
duration = 10,
type = "error"
)
} else {
if (length(list.files(
dirFilteringDownloadPath(),
"*fastq$|*fq$|*fastq.gz$|*fq.gz$"
)) > 1) {
} else {
#start time to monitor execution
start_time_filtering(Sys.time())
shinyjs::disable("Filtering")
shinyjs::enable("killFiltering")
tryCatch({
rvFil$Filtering_process <- callr::r_bg(
func = Filtering
,
args = list(
Nodes = input$filteringThreads,
X = ListFIlter(),
UploadPath = file.path(dirFilteringUploadPath(), "/"),
DownloadPath = file.path(dirFilteringDownloadPath(), "/"),
qualityType = input$QualityTypeFiltering,
minLen = input$minLen,
trim = input$trim,
trimValue = input$trimValue,
n = input$nChunk,
Adapters = input$Adapters,
Lpattern = input$Lpattern,
Rpattern = input$Rpattern,
max.Lmismatch = input$max.Lmismatch,
max.Rmismatch = input$max.Rmismatch,
kW = input$kW,
left = input$left,
right = input$right,
halfwidthAnalysis = input$halfwidthAnalysis,
halfwidth = input$halfwidth,
compress = input$compress
)
,
supervise = TRUE
,
error = getOption("callr.error", "error")
)
}
, error = function(e) {
shiny::showNotification(
"error occours - check if files with the name of the samples already exist in selected folder",
action = NULL,
duration = NULL,
closeButton = TRUE,
id = NULL,
type = "error"
)
}) # End of tryCatch
shiny::showNotification(
"Filtering analysis has been started",
action = NULL,
duration = 10,
closeButton = TRUE,
id = NULL,
type = "message"
)
}
}
})
# Output the status of the filtering process
shiny::observeEvent(input$Filtering, {
if (is.integer(input$directoryRawReadsFilteringUpload) ||
is.integer(input$directoryRawReadsFilteredDownload)) {
# No action needed if directories are not selected
} else {
if (length(list.files(
dirFilteringDownloadPath(),
"*fastq$|*fq$|*fastq.gz$|*fq.gz$"
)) > 1) {
} else {
output$CheckStatusOut <- shiny::renderPrint({
shiny::req(input$Filtering)
if (shiny::isolate(rvFil$Filtering_process$is_alive()) == TRUE) {
# autoInvalidate()
shiny::invalidateLater(5000)
rvFil$Filtering_process$print()
cat(
shiny::isolate(
"This process could be time-consuming\nFeel free to take a coffee break\n\n ( (\n ) )\n ..........\n | |]\n \\ /\n '----'"
)
)
} else {
#check end time of process
end_time_filtering <- Sys.time()
execution_time_filtering <- end_time_filtering - start_time_filtering()
# Convert to hours, minutes, and seconds
execution_time_sec_filtering <- as.numeric(execution_time_filtering, units="secs")
hours_filtering <- floor(execution_time_sec_filtering / 3600)
minutes_filtering <- floor((execution_time_sec_filtering %% 3600) / 60)
seconds_filtering <- execution_time_sec_filtering %% 60
# Print the result
cat(paste(shiny::isolate("The filtering analysis has been completed!\n")),"Execution Time: ", hours_filtering, "hours", minutes_filtering, "minutes", round(seconds_filtering, 2), "seconds\n")
# shinyjs::enable and shinyjs::disable button
shinyjs::enable("Filtering")
shinyjs::disable("killFiltering")
}
})
}
}
})
# Interrupt the filtering process if the kill button is clicked
shiny::observeEvent(input$killFiltering, {
# stop the slow Filtering() function
rvFil$Filtering_process$kill() #Terminate the process. It also terminate all of its child processes, except if they have created a new process group (on Unix), or job object (on Windows). It returns TRUE if the process was terminated, and FALSE if it was not (because it was already finished/dead when processx tried to terminate it).
shinyjs::enable("Filtering")
shinyjs::disable("killFiltering")
output$CheckStatusOut <- shiny::renderPrint({
shiny::invalidateLater(5000)
# autoInvalidate()
if (shiny::isolate(rvFil$Filtering_process$is_alive()) == FALSE) {
cat(shiny::isolate("The filtering analysis has been killed!"))
unlink(logFile())
}
})
shiny::showNotification(
"The filtering analysis has been killed!",
action = NULL,
duration = 10,
closeButton = TRUE,
id = NULL,
type = "warning"
)
})
shiny::observe({
# Check if the download directory is empty to avoid overwriting files
if (length(list.files(
dirFilteringDownloadPath(),
"*fastq$|*fq$|*fastq.gz$|*fq.gz$"
)) > 1) {
shiny::showNotification(
"The folder already contains FASTQ files - select an empty folder",
action = NULL,
duration = NULL,
closeButton = TRUE,
id = NULL,
type = "warning",
session = getDefaultReactiveDomain()
)
}
})
shiny::observeEvent(input$Filtering, {
shiny::req(dirFilteringUploadPath())
shiny::req(dirFilteringDownloadPath())
if (length(list.files(dirFilteringDownloadPath(), "*fastq$|*fq$|*fastq.gz$|*fq.gz$")) > 1) {
shiny::showNotification(
"The folder already contains FASTQ files - select an empty folder",
type = "error",
duration = NULL
)
} else {
# Reactive polling to check for new files
dataFiltering <- shiny::reactivePoll(
5000,
session,
checkFunc = function() {
files <- list.files(dirFilteringDownloadPath(), "*fastq$|*fq$|*fastq.gz$|*fq.gz$", full.names = TRUE)
if (length(files) > 0) {
return(max(file.info(files)$mtime))
}
return(Sys.time()) # Avoid NULL return
},
valueFunc = function() {
files <- list.files(dirFilteringDownloadPath(), "*fastq$|*fq$|*fastq.gz$|*fq.gz$", full.names = TRUE)
if (length(files) == 0) {
return(data.frame(
files = character(),
`size (gb)` = numeric(),
`mtime (y-m-d_h-m-s)` = character(),
Processed = numeric(),
Retained = numeric(),
Discarded = numeric(),
`Discarded_%` = character()
))
}
info <- file.info(files)
info$size <- info$size / 1e9
info$files <- basename(rownames(info))
info <- dplyr::select(info, c("files", "size", "mtime")) %>%
dplyr::rename(
"size (gb)" = "size",
"mtime (y-m-d_h-m-s)" = "mtime"
)
empty_df_with_na <- data.frame(
col1 = NA, # Column 1 (NA value)
col2 = NA, # Column 2 (NA value)
col3 = NA, # Column 3 (NA value)
col4 = NA # Column 4 (NA value)
)
info <- cbind(info,empty_df_with_na)
fileslog <- list.files(dirFilteringDownloadPath(), "*.log$", full.names = TRUE)
logFile(fileslog)
if (length(fileslog) > 0) {
resultSum <- sapply(fileslog, function(i) {
df <- utils::read.table(i)
name <- unique(df$V1)
processStats <- function(name) {
df1sum <- df %>% filter(V1 == name) %>% select(2:4) %>% apply(., 2, sum)
percentDiscarded <- paste0(round(as.numeric(df1sum[3]) * 100 / as.numeric(df1sum[1]), 2), "%")
return(c(name, df1sum, percentDiscarded))
}
df1 <- processStats(name[[1]])
df2 <- processStats(name[[2]])
df <- rbind(df1, df2) %>%
`colnames<-`(c("files", "Processed", "Retained", "Discarded", "Discarded_%"))
return(df)
}, simplify = FALSE, USE.NAMES = TRUE) %>% do.call(rbind, .)
info <- dplyr::left_join(info[1:3], data.frame(resultSum), by = "files")
}
return(info)
}
)
output$FilteredSample <- DT::renderDT(
dataFiltering(),
selection = 'none',
editable = FALSE,
rownames = FALSE,
colnames = c("files",
"size (gb)",
"mtime (y-m-d_h-m-s)",
"Processed",
"Retained",
"Discarded",
"Discarded_%"),
extensions = 'Buttons',
options = list(
paging = FALSE,
searching = TRUE,
fixedColumns = TRUE,
autoWidth = TRUE,
ordering = TRUE,
dom = 'Bfrtip',
buttons = list(
list(extend = 'csv', title = "FilteringResult")
)),
class = "display"
)
}
})
} # close function inside moduleServer
) # close moduleServer
} # close IndexingBulkServerLogic function
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