shiny/globals.R

In uit-bdps/pippeline: Pipeline for processing high-dimensional multi-omics biobank datasets

# globals, all sessions

# pipeline: basics
basics <- list(appName = "Pippeline", 
               title = "Biobank Dataset Processing Script & Report", 
               optionsFile = "options.csv", 
               questsFile = "questionnaires.txt",
               docFormat = "html",  # note: pandoc'ing with target PDF is buggy in R 3.2.3, rmarkdown 1.4, pandoc 1.16.0.2
               msgDuration = 7, 
               ids = c("lpnr", "labnr", "serienr")) # ID labels to remove before data are written



# tabs
critTabsId <- c("outliers", "corr", "filter", "norm", "quest", "process", 
                "divd")

# strings
procMsg <- "First, you need to enter basic information and make your choices."
notSelOpt <- "Not selected"
notEnablOpt <- "Not enabled"
notProcMsg <- "Dataset is not processed"

# Slurm job id (can be SLURM_JOBID)
jobID <- Sys.getenv("SLURM_JOB_ID")

pipFolder <- "/pippelinen"
pipProjects <- file.path(pipFolder, "projects")
nowacleanOutliers <- file.path(pipFolder, "nowaclean_outliers", "outliers")
nowacleanReports <- file.path(pipFolder, "nowaclean_outliers", "reports")
deathInfoFile <- file.path(pipFolder, "utility", "death_causes", "DI280119.csv")

cctransExcl <- file.path(pipFolder, "transition_information", "to_exclude")
cctransReports <- file.path(pipFolder, "transition_information", "reports")

# determine options for basic choices
options <- NULL
tryCatch({
  options <- read.csv(basics$optionsFile)
}, error = function(err) {
  showNotification(paste0("Error while loading file ", basics$optionsFile, 
                          ". (Wrong format?) Error code #5.", type = "error", duration = basics$msgDuration))
})
dsgs <- c(notSelOpt, levels(options[, "Design"]))
locs <- c(notSelOpt, levels(options[, "Location"]))
mats <- c(notSelOpt, levels(options[, "Material"]))
anas <- c(notSelOpt, levels(options[, "Analysis"]))

outls <- list.files(nowacleanOutliers, pattern = "\\.rds$")
outls <- c(notSelOpt, outls)

outls_rprts <- list.files(nowacleanReports, pattern = "\\.html$")
outls_rprts <- c(notSelOpt, outls_rprts)

trns <- list.files(cctransExcl, pattern = "\\.rds$")
trns <- c(notSelOpt, trns)

trns_rprts <- list.files(cctransReports, pattern = "\\.html$")
trns_rprts <- c(notSelOpt, trns_rprts)

# Batching
btchtab <- c(notSelOpt)
btchvar <- c(notSelOpt)

quests <- NULL
tryCatch({
  quests <- readLines(basics$questsFile)
}, error = function(err) {
  showNotification(paste0("Error while loading file ", basics$questsFile, 
                          ". (Wrong format?) Error code #6.", type = "error", duration = basics$msgDuration))
})
quests <- c(notSelOpt, quests)
qvars <- NULL

nmeths <- c(notSelOpt, "vstQuantileNorm", "ComBat")

# JavaScript
jscode <- "
shinyjs.closeWindow = function() { window.close(); }

shinyjs.disableTab = function(name) {
  var tab = $('.nav li a[data-value=' + name + ']');
  tab.bind('click.tab', function(e) {
    e.preventDefault();
    return false;
  });
  tab.addClass('disabled');
}

shinyjs.enableTab = function(name) {
  var tab = $('.nav li a[data-value=' + name + ']');
  tab.unbind('click.tab');
  tab.removeClass('disabled');
}
"