################################################################################
## Project PuMaQC - pipeline
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
## This is the main controlling script
##
## (c)GNU GPL P.V.Nazarov, J.P.Corte-Real
################################################################################

#ini.file = "f:/Data/PuMaQC/testStudy1/project.ini"
#src.path = "n:/Develop/R/PipeLines/PuMaQC.b"

PuMaQC = function(ini.file="<empty>",src.path = "http://sablab.net/PuMaQC") {

  source(file.path(src.path,"PuMaQC.Search.r"))
  source(file.path(src.path,"PuMaQC.Download.r"))
  source(file.path(src.path,"PuMaQC.Preprocessing.r"))
  source(file.path(src.path,"PuMaQC.QC.r"))
  source("http://sablab.net/scripts/parseINI.r")

  st.title =
c("\n ##################################################\n",
     "##                P u M a Q C                   ##\n",
     "##-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=##\n",
     "## PuMAQC - Public Microarray Quality Control   ##\n",
     "## tool provides a simple pipeline for querying ##\n",
     "## and downloading Affymetrix data from GEO,    ##\n",
     "## followed by preprocessing, quality control   ##\n",
     "## and report generation.                       ##\n",
     "##-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=##\n",
     "## (c)GNU GPL P.V.Nazarov, J.P.Corte-Real, 2011 ##\n",
     "##################################################\n")
     cat(st.title)

  ## Check whether INI file exists and validate its structure
  while (T){
    cat("\n\n")
    cat("Your initialization file is:\n>>  ")
    cat(ini.file)
    cat("\nPress ENTER if it is correct or type new file name (ESC/Ctrl-C for exit):\n")
    key = scan(n=1,what="")
    key = ifelse(length(key)==0,ini.file,key)
    cat("\nTrying to open ",key," ... ")
    if (file.exists(key)){
      cat("FOUND.\n")
      ini.file=key
    } else {
      cat("NOT FOUND! Redefine file location, please.\n")
      next
    }

    ## Validate INI file
    Info = parseINI(ini.file,correct.bslash=T)
    fields.need = c("Project$Title",
                  "Search$GEOmetadb","Search$Platform","Search$Organism",
                  "Search$Results","Import$DownloadTo","Import$CDF","Import$APT")
    fields.ini = character(0)
    for (i in 1:length(Info)) fields.ini=c(fields.ini,paste(names(Info)[i],names(Info[[i]]),sep="$"))
    if (sum(!(fields.need %in% fields.ini))>0) {
      cat("Some fields are missed in INI file:", fields.need[!(fields.need %in% fields.ini)],"\n")
      next
    }
    cat("INI file structure seems to be correct.\n")

## ToDo! Check APT tools
## ToDo! Check paths in INI - no spaces
## ToDo! Check that at least one include key is given

    break
  } # INI file check

  ## set default folder to the same folder as INI, if we are not there already
  if (length(grep("/",ini.file))>0){
    setwd(sub("/[^/]+$","",ini.file))
  }else{
    ini.file = file.path(getwd(),ini.file)
  }  

################################################################################
## Libraries: check installed libraries and install what is necessary
################################################################################

  selectOption = function (txt="Enter:",opt=c(letters,0:9)){
    ans=""
    repeat{
      cat("\n")
      cat(txt)
      ans = scan(n=1,what="")
      if (length(ans)==0)ans=""
      ans=casefold(ans)
      if (ans %in% opt) break
      cat("...not recognized. Please repeat\n")
    }
    return(ans)
  }

  installed = as.data.frame(installed.packages(), stringsAsFactors=F)$Package
  required = c("GEOquery","GEOmetadb","arrayQualityMetrics","R.utils")
  idx.to.install = which(!(required %in% installed))

  if (length(idx.to.install)>0){
    cat("The following libraries are not installed:",paste(required[idx.to.install],collapse=", "),"\n")
    ans = selectOption("Would you like to do this now? (Y/n): ",c("","y","n"))
    if (ans=="y"|ans=="") {
      source("http://bioconductor.org/biocLite.R")
      for (i in idx.to.install)
        biocLite(required[i])
    }else{
      cat("Ok. But they may be required for different steps of analysis later\n")
    }
  }

################################################################################
## Operation Loop
################################################################################
  while(T){

  status = data.frame(matrix(-1,nc=3,nr=4))
  names(status)=c("part","code","text")
  status$part=c("Search","Download","Preprocessing","QC")
  
  Meta=data.frame(matrix(nc=2,nr=2))
  if (file.exists(Info$Search$Results)) {
    status$code[1] = 1
    Meta=read.table(Info$Search$Results,header=T,sep="\t",comment.char="",quote="\"",as.is=T)
  }else status$code[1] = 0
  if (length(grep("PuMaQC",names(Meta)))>0) status$code[2] = 1
  if (file.exists(Info$Import$Results)) status$code[3] = 1;
  if (file.exists(Info$QC$Results)) status$code[4] = 1;
  
  for ( i in which(status$code== -1)){
    if (status$code[i-1]==1) status$code[i]=0
  }

  status$text = c("not allowed","not done","done")[status$code+2]

  while(T){
    cat("\n\n")
    cat("========================================================\n")
    cat("PuMaQC is ready to work. Select one of the options:\n")
    cat("  1. GEO Search (",status$text[1],")\n")
    cat("  2. Data Download and Unpack (",status$text[2],")\n")
    cat("  3. Data Preprocessing (",status$text[3],")\n")
    cat("  4. Quality Control (",status$text[4],")\n")
    cat("  5. Run complete pipeline (1-4)\n")
    cat("  0. Exit (or ESC / Ctrl-C)")
    key = as.integer(selectOption("Choose action: ",0:5))
    if (key==0) break
    if (key==5) break
    if (status$code[key]>=0) break
    cat("this action cannot be performed yet.\n")
  }
  if (key==0) break
  ##=================
  ## SEARCH
  if (key==1 | key==5) {
    cat("\n")
    cat("######################################################\n")
    cat("##                   PuMaQC: SEARCH                 ##\n")
    cat("######################################################\n")
   
    # load libraties
    library(GEOquery)
    library(GEOmetadb)

    setwd(sub("/[^/]+$","",ini.file))
    Info = parseINI(ini.file, correct.bslash=T)

    # download GEOmetadb.sqlite file if it does not exist
    if (is.null(Info$Search$GEOmetadb)) Info$GEOmetadb=""
    if (file.exists(Info$Search$GEOmetadb)){
      if (file.info(Info$Search$GEOmetadb)$size<2^30){
        cat("\nIncomplete GEOmetadb.sqlite file is detected. Removing...\n\n")
        file.remove(Info$Search$GEOmetadb)
      }
    }

    if (!file.exists(Info$Search$GEOmetadb)){
      try(getSQLiteFile(destdir = sub("/[^/]+$","",Info$Search$GEOmetadb),
                        destfile = paste(sub("^.+/","",Info$Search$GEOmetadb),".gz",sep="")))
      ## manual download
      #  download.file("http://gbnci.abcc.ncifcrf.gov/geo/GEOmetadb.sqlite.gz",method="internal",destfile = "GEOmetadb.sqlite.gz",mode="wb")
      #  R.utils::gzip("GEOmetadb.sqlite.gz", destname="GEOmetadb.sqlite", overwrite=F)
    }
    flush.console()
    try(dev.off(), silent = TRUE)
    try(PuMaQC.Search(ini.file,src.path))
    try(dev.off(), silent = TRUE)
    warnings()
    cat("\nFinished.\nSee PuMaQC-1_Search.pdf for the report\n")
    cat("See and modify ",Info$Search$Results," file for manual data exclusion.\n")
  }

  ## IMPORT
  if (key==2 | key==5) {
    cat("\n")
    cat("######################################################\n")
    cat("##                   PuMaQC: Download               ##\n")
    cat("######################################################\n")
    flush.console()
    try(dev.off(), silent = TRUE)
    try(PuMaQC.Download(ini.file,src.path))
    try(dev.off(), silent = TRUE)
    warnings()
    cat("\nFinished.\n")
  }

  ## PREPROCESSING
  if (key==3 | key==5) {
    cat("\n")
    cat("######################################################\n")
    cat("##                   PuMaQC: PREPROCESSING          ##\n")
    cat("######################################################\n")
    flush.console()
    try(dev.off(), silent = TRUE)
    try(PuMaQC.Preprocessing(ini.file,src.path))
    try(dev.off(), silent = TRUE)
    warnings()
    cat("\nFinished.\n")
  }

  ## QC
  if (key==4 | key==5) {
    cat("\n")
    cat("######################################################\n")
    cat("##                   PuMaQC: QC                     ##\n")
    cat("######################################################\n")
    flush.console()
    try(dev.off(), silent = TRUE)
    try(PuMaQC.QC(ini.file,src.path))
    try(dev.off(), silent = TRUE)
    warnings()
    cat("\nFinished.\n")
  }

 } # operating loop

}