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Address several issues/bugs.
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aprice committed Oct 17, 2024
1 parent 87c8f9e commit e8b510a
Showing 1 changed file with 129 additions and 38 deletions.
167 changes: 129 additions & 38 deletions inst/application/server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,8 @@ function(input, output, session) {
selected_counts_file <- reactiveVal(NULL)
skipSampleChange <- reactiveVal(FALSE)

restricted_paths <- c("/juno/work/ccs/shared/resources/")

session_data <- reactiveValues(
personal_storage_path = NULL,
mount_refit_path = NULL,
Expand Down Expand Up @@ -310,7 +312,6 @@ function(input, output, session) {

observeEvent(input$button_samplesInput, {

print("SAMPLES")
# Get the input from textAreaInput_samplesInput and clean it up
input_text <- input$textAreaInput_samplesInput

Expand Down Expand Up @@ -442,6 +443,14 @@ function(input, output, session) {
}
)



# Function to check if the given path is restricted
is_restricted_path <- function(check_path) {
# Check if the path contains any of the restricted paths
any(sapply(restricted_paths, function(restricted) grepl(restricted, check_path)))
}

# Function to check if a given local path represents a remote file
is_remote_file <- function(local_path) {
# Get the mount information
Expand Down Expand Up @@ -592,6 +601,18 @@ function(input, output, session) {
return()
}

# Check if storageType is Personal (FALSE) and if personal_storage_path is empty
if (!input$storageType && session_data$personal_storage_path == "") {
showNotification("Invalid personal repository configuration.", type = "error")

# Set the value of storageType back to TRUE (Remote)
updateSwitchInput(session, "storageType", value = TRUE)

return() # Exit function after resetting the storageType
}

#session_data$personal_storage_path

if (input$storageType) {
#print("Storage Type is set to Remote")

Expand Down Expand Up @@ -789,6 +810,17 @@ function(input, output, session) {
return()
}

# Check if storageType is Personal (FALSE) and if personal_storage_path is empty
if (!input$storageType_compare && session_data$personal_storage_path == "") {
showNotification("Invalid personal repository configuration.", type = "error")

# Set the value of storageType back to TRUE (Remote)
updateSwitchInput(session, "storageType_compare", value = TRUE)

return()
}


if (input$storageType_compare) {
#print("Storage Type is set to Remote")

Expand Down Expand Up @@ -1093,7 +1125,9 @@ function(input, output, session) {

#Hide/show refit box when necessary.
observe({
if ((session_data$password_personal == 1 && !input$storageType) || session_data$password_valid == 1 || !is_remote_file(selected_sample_path)) {
if ((session_data$password_personal == 1 && !input$storageType) ||
session_data$password_valid == 1 ||
(is_remote_file(selected_sample_path) && !is_restricted_path(get_remote_path(selected_sample_path)))) {
shinyjs::show("fitPanel")
if(input$session_remote_refit)
{
Expand Down Expand Up @@ -1138,7 +1172,7 @@ function(input, output, session) {

if (nrow(matched_row) > 0) {
# Check if the remote_path contains "/juno/work/"
if (any(grepl("/juno/work/", matched_row$remote_path))) {
if (is_restricted_path(matched_row$remote_path)) {
if (session_data$password_valid == 1 || !is_remote_file(selected_sample_path)) {
showNotification("You are authorized to make changes to this sample.", type = "message")
} else {
Expand Down Expand Up @@ -1297,7 +1331,9 @@ function(input, output, session) {

#Hide/show refit box when necessary.
observe({
if ((session_data$password_personal == 1 && !input$storageType) || session_data$password_valid == 1 || !is_remote_file(selected_sample_path)) {
if ((session_data$password_personal == 1 && !input$storageType) ||
session_data$password_valid == 1 ||
(is_remote_file(selected_sample_path) && !is_restricted_path(get_remote_path(selected_sample_path)))) {
shinyjs::show("fitPanel")
if(input$session_remote_refit && is_remote_file(selected_sample_path))
{
Expand Down Expand Up @@ -3028,6 +3064,12 @@ function(input, output, session) {
valid_tcga_repo <- validate_path(repository_path_tcga) && (!input$session_switch_tcga || repository_path_tcga != "")
valid_tcga_remote <- validate_path(remote_path_tcga) && (!input$session_switch_tcga || remote_path_tcga != "")

# Check if personal_storage_path is a remote file, don't let them write to mounted locations this way.
if (is_remote_file(personal_storage_path)) {
showNotification("Personal repository cannot be a mounted directory. Use a local directory instead.", type = "error")
personal_storage_path <- "" # Set personal_storage_path to an empty string
}

# Check all validations and print errors if any
if (!valid_personal_storage){
showNotification("Invalid or missing local storage path.", type = "error")
Expand Down Expand Up @@ -3202,10 +3244,27 @@ function(input, output, session) {


set_default_countFile <- function() {
selected_run <- values$sample_runs %>% filter(fit_name == 'default') %>% head(n = 1)
# Check the number of rows in values$sample_runs
if (nrow(values$sample_runs) == 1) {
# If only one row, use that one
selected_run <- values$sample_runs
} else {
# If more than one row, try to filter for 'default'
selected_run <- values$sample_runs %>%
filter(fit_name == 'default') %>%
head(n = 1)

if (nrow(selected_run) == 0) {
selected_run <- values$sample_runs[which(values$sample_runs$fit_name == paste0(input$selectInput_selectFit)),]
# If no exact 'default' match, look for any fit_name containing 'default'
if (nrow(selected_run) == 0) {
selected_run <- values$sample_runs %>%
filter(grepl('default', fit_name, ignore.case = TRUE)) %>%
head(n = 1)
}

# If still no match, use the first row
if (nrow(selected_run) == 0) {
selected_run <- values$sample_runs %>% head(n = 1)
}
}

run_path <- selected_run$path[1]
Expand All @@ -3215,60 +3274,92 @@ function(input, output, session) {
roots <- c(current_run = run_path)
shinyFiles::shinyFileChoose(input, "fileInput_pileup", roots = roots, filetypes = c('dat', 'gz'))

# Try to find files that match the expected pattern for countsMerged files
counts_file_name <- glue::glue("{run_path}/countsMerged____{sample_id}.dat.gz")

if (file.exists(counts_file_name)) {
# Set the selected counts file path in the reactive value
# Set the selected counts file path in the reactive value if the exact file exists
selected_counts_file(counts_file_name)
} else {
# If the file does not exist, search for alternatives
files_in_directory <- list.files(run_path, pattern = "(countsMerged|\\.dat\\.gz)$", full.names = TRUE)
# If no file matches the exact pattern, look for any file with "count" in the name
files_in_directory <- list.files(run_path, pattern = "count", full.names = TRUE, ignore.case = TRUE)

if (length(files_in_directory) > 0) {
# Use the first matching file
selected_counts_file(files_in_directory[1])
} else {
showNotification("No suitable countsMerged file found in the run directory.", type = "warning")
# If no "count" file is found, look for any .gz file
gz_files_in_directory <- list.files(run_path, pattern = "\\.gz$", full.names = TRUE)

if (length(gz_files_in_directory) > 0) {
# Use the first .gz file if available
selected_counts_file(gz_files_in_directory[1])
} else {
# If no .gz file is found, use any file in the directory
all_files_in_directory <- list.files(run_path, full.names = TRUE)

if (length(all_files_in_directory) > 0) {
# Use the first file in the directory as a fallback
selected_counts_file(all_files_in_directory[1])
}

# Show a notification that no suitable counts files were found, at this point its the user's problem.
showNotification(paste0("No suitable countsMerged or .gz files found in the run directory at ",run_path), type = "warning")
}
}
}
#showNotification(paste("Selected counts file is", selected_counts_file()), type = "message")
}




observeEvent(input$fileInput_pileup, {
# Filter the selected run and determine the run path
selected_run <- values$sample_runs %>% filter(fit_name == 'default') %>% head(n = 1)
# Check the number of rows in values$sample_runs
if (nrow(values$sample_runs) == 1) {
# If only one row, use that one
selected_run <- values$sample_runs
} else {
# If more than one row, try to filter for 'default'
selected_run <- values$sample_runs %>%
filter(fit_name == 'default') %>%
head(n = 1)

if (nrow(selected_run) == 0) {
selected_run <- values$sample_runs[which(values$sample_runs$fit_name == paste0(input$selectInput_selectFit)),]
}
# If no exact 'default' match, look for any fit_name containing 'default'
if (nrow(selected_run) == 0) {
selected_run <- values$sample_runs %>%
filter(grepl('default', fit_name, ignore.case = TRUE)) %>%
head(n = 1)
}

run_path <- selected_run$path[1] # Get the first path
# If still no match, use the first row
if (nrow(selected_run) == 0) {
selected_run <- values$sample_runs %>% head(n = 1)
}
}

# Set up shinyFileChoose with the current run path as the root
shinyFiles::shinyFileChoose(input, "fileInput_pileup", roots = c(current_run = run_path), session = session)
# Check if the selected row has a valid path and is not NA
if (!is.null(selected_run$path) && length(selected_run$path) > 0 && !is.na(selected_run$path[1])) {
run_path <- selected_run$path[1] # Get the first path
# Set up shinyFileChoose with the current run path as the root
shinyFiles::shinyFileChoose(input, "fileInput_pileup", roots = c(current_run = run_path), session = session)

# Parse the file path selected by the user
file_info <- shinyFiles::parseFilePaths(roots = c(current_run = run_path), input$fileInput_pileup)
# Parse the file path selected by the user
file_info <- shinyFiles::parseFilePaths(roots = c(current_run = run_path), input$fileInput_pileup)

# Extract the file path as a character string
file_path <- as.character(file_info$datapath)
# Extract the file path as a character string
file_path <- as.character(file_info$datapath)

# Check if file_path is valid and update the reactive value
if (!is.null(file_path) && length(file_path) > 0 && file_path != "") {
selected_counts_file(file_path) # Set the selected file path
showNotification(paste("Selected counts file is", selected_counts_file()), type = "message")
# Check if file_path is valid and update the reactive value
if (!is.null(file_path) && length(file_path) > 0 && file_path != "") {
selected_counts_file(file_path) # Set the selected file path
showNotification(paste("Selected counts file is", selected_counts_file()), type = "message")
}
} else {
showNotification("No valid run path found", type = "error")
}
})


observeEvent(input$create_folder_button, {
personal_storage_path <- input$personal_storage_path
if (!dir.exists(personal_storage_path)) {
dir.create(personal_storage_path, recursive = TRUE)
}
updateTextInput(session, "personal_storage_path", value = personal_storage_path)
shinyjs::hide("invalid_path_message")
shinyjs::hide("create_folder_button_container")
})


observeEvent(input$mount_refit_path, {
Expand Down Expand Up @@ -3691,7 +3782,7 @@ function(input, output, session) {

if (nrow(matched_row) > 0) {
# Check if the remote_path contains "/juno/work/"
if (any(grepl("/juno/work/", matched_row$remote_path))) {
if (is_restricted_path(matched_row$remote_path)) {
if (session_data$password_valid == 1 || !is_remote_file(selected_sample_path)) {
showNotification("Authorized Refit.", type = "message")
} else {
Expand Down

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